When Palo Alto officials learned in early 2009 that a little-known Sacramento agency had developed plans to build a 15-foot wall along the Caltrain tracks to support a planned high-speed-rail system, surprise quickly gave way to confusion and anger.

How could it be, many wondered, that a statewide project that just months ago earned the enthusiastic endorsement of the entire City Council and the approval of California voters now threatened to divide the city? More critically, why wasn't the city consulted?

Tempers simmered through January and February and finally came to a boil in March, after the City Council heard a presentation from Rod Diridon, one of two Bay Area representatives from the California High-Speed Rail Authority. His message was clear: High-speed rail will run through Palo Alto. Though the authority hadn't yet made a final decision about elevated tracks versus underground tunnels, its choice of the route was set in stone. Would the rail authority be willing to reopen its environmental analysis and reconsider this decision, former Councilwoman Yoriko Kishimoto asked? Diridon said no, leaving council members fuming.

"Seems to me they're on an express train, and we're on a bicycle trying to catch up," then Vice Mayor Jack Morton observed at the March 2 meeting, which was followed in rapid order by citizen protests, lawsuits, births of new grassroots organizations, intense lobbying in Sacramento, an official Palo Alto vote to oppose high-speed rail and, once the dust settled, a decision by the rail authority to scrap the dreaded four-track plan for the San Francisco Peninsula in favor of a more palatable "blended system," in which Caltrain and high-speed rail would share a single set of electrified tracks.

The city's long and expensive battle against high-speed rail was the most extreme, but far from only, example of an ongoing Palo Alto frustration — the city's inability to influence the regional forces that threaten to profoundly change it. On any given week, the council could be discussing the Association of Bay Area Governments' (ABAG) mandate that the city plan for thousands more residences despite its acute traffic and parking problems; the Santa Clara Valley Transportation Authority's (VTA's) soon-to-unfold "Bus Rapid Transit" system that will turn El Camino Real into a regional bus highway; or Caltrain's long-awaited electrification, which would greatly increase the number of trains and riders arriving at the University Avenue station every morning. Each of these agencies is headed by a board of directors composed of elected leaders from stakeholder jurisdictions. In each case, Palo Alto is a major stakeholder. Oddly enough, not a single one of these boards includes a Palo Alto council member.

This lack of influence is particularly striking given Palo Alto's outsized reputation as a global trend-setter. Its image as high-tech Mecca — inflated over the decades by the likes of Hewlett-Packard, Google and Facebook and nurtured today by the likes of Tesla, Palantir and VMWare — means the city has plenty of friends in high places around the world. Jet-lagged mayors and ambassadors from distant lands — Shanghai, New Zealand, Heidelberg — have made recent pilgrimages to University Avenue and Page Mill Road, eager to learn about digital culture and environmental stewardship.

And it's not just wonks and environmentalists. Hundreds of mourners with iPhones flocked to Old Palo Alto after the city's most famous resident, Steve Jobs, died in 2011, leaving flowers and notes near his home and bestowing the kind of devotion once reserved for the bones of saints in Canterbury Cathedral. Two other local tech titans, Larry Page and Mark Zuckerberg, made global news by, respectively, adding a basement and buying up neighboring properties. No wonder Vanity Fair had recently describe the city as the "Rome of our nascent millennium."

Even so, Palo Alto may as well be Rome when it comes to dealing with issues in its own Silicon Valley backyard. On one issue after another, from bus transit and rail service to housing mandates and employee pensions, the city has been relegated to the sidelines, free to submit comments but devoid of any decision-making authority. On the Caltrain board of directors, for instance, Palo Alto holds less sway than Gilroy, a city with about 50,000 residents and great garlic. This despite the fact that Palo Alto boasts the second busiest Caltrain station in the entire system, trailing only San Francisco.

Palo Alto's problem is that it's a small city with big-city problems — too much traffic, too little parking, increasingly dense building and people living in their cars. Like a successful city, it has high ambitions, a wealth of jobs and a vibrant, rapidly evolving restaurant scene. But as a suburb with about 65,000 residents, it lacks the tools most big cities have for dealing with urban problems. Palo Alto's municipal transportation system consists of two shuttles. Its newly adopted program for dealing with homelessness was developed largely by the nonprofit community and leans heavily on county grants.

The city's small size has often made it hard for local officials to win regional influence. Representation on many regional boards and on the county Board of Supervisors functions less like the U.S. Senate and more like the U.S. House of Representatives, with population as the driving influence. It makes no difference that Stanford University is literally across the street and that the city's population balloons (either doubles or triples, depending on the estimate) during business hours. When it comes to representation and influence, it's the residing population that counts. And San Jose, the county giant with its close to a million residents, gobbles up most of the seats and much of the influence on local boards. Councilwoman Liz Kniss, who in her prior position on the Santa Clara County Board of Supervisors served both on the Caltrain and the VTA boards, said Palo Alto was often marginalized in county matters as a small, wealthy city far up north.

"It's easy to shut us out because we're way up here," Kniss said in a recent interview. "There is San Jose, which literally overpowers every other city. Even as a county supervisor, I had a very hard time getting resources at this end of the county."

But while Palo Alto continues to have a representative on the county board — former Palo Alto mayor and state Senator Joe Simitian was elected in 2012 after terming out of Sacramento — its influence on other regional policymaking boards has often been nonexistent.

Current Palo Alto Mayor Greg Scharff was unequivocal when asked last week whether he feels the city is adequately represented on regional and state issues. He said in an email that he didn't know the last time the city had a representative on any of the major transit boards or on ABAG, where he now serves as an alternate, a position that allows him to attend meetings when the regional Santa Clara County representative can't make it.

"The city is definitely under-represented on all regional agencies," Scharff said.

Some remedies, however, may be afoot. On Oct. 7, the City Council unanimously nominated one of its members, Gail Price, to serve on the board of the VTA, an appointment that is expected to get the regional board's approval in November. Vice Mayor Nancy Shepherd, following the example of veteran Councilman Larry Klein, has been making the rounds at the League of California Cities and swapping ideas and experiences with other mayors and council members. And Kniss earlier this year co-signed a memo with Price and Shepherd calling for the city to extend the number of consecutive terms a council member can serve from two to three, a move designed to improve the city's chance of getting one of its council members a leadership position on a regional board.

For the past four years, Gail Price has been patiently paying her dues on the VTA. In early November, she is due to reap the rewards.

Since 2009, Price has been serving on the VTA's Policy Advisory Committee, a group of local officials that reviews proposed policies and submits recommendations to the VTA board of directors, which then makes a decision. In 2012, she served as the committee's vice chair. This year, she chaired the committee, a job that required her to make summary presentations to the board, explaining the committee's recommendation. If all goes as planned, the former transportation planner will next month join the actual board as a representative of Group 2, which includes Palo Alto, Mountain View, Los Altos and Los Altos Hills.

The appointment is significant for several reasons. As the county's primary transportation agency, the VTA controls vital transit services, including the well-used 22 bus line that runs along El Camino Real in Palo Alto. More importantly, it controls funds. While the bulk of federal grants get distributed by the Metropolitan Transportation Commission, another powerful regional association on which Palo Alto has no voice, it is the VTA that considers the proposals from cities and makes a recommendation to the MTC on which projects to fund. Projects such as Palo Alto's soon-to-commence reduction of lanes on California Avenue from four to two and the recently introduced bike-share program were both funded through MTC grants administered by the VTA.

As a board member, Price will have a say in these matters, as well as on the VTA's rollout of the "Bus Rapid Transit" system, which is already starting in the San Jose area and which is set to ultimately make its way up to the northern part of the county.

Membership on the VTA board will also make Price eligible for one of the coveted positions on the Peninsula Corridor Joint Powers Board, which administers Caltrain. The board is composed of nine members, with San Francisco, San Mateo and Santa Clara counties each getting three seats. In Santa Clara County, it is the VTA that decides whom to send to the Caltrain board. Today, all three members — Supervisor Ken Yeager, San Jose Councilman Ash Kalra and Gilroy Councilman Perry Woodward — are from the southern end of the county.

Palo Alto's lack of representation on the Caltrain board has long been a source of consternation for council members, who feel that ridership should play a factor in representation. Price is among them.

"Logic would suggest that there should be greater attention paid to cities that have the greatest ridership numbers," Price said, referring to Palo Alto's popular University Avenue depot. "To be truly representative of the users of Caltrain, the high-use Caltrain stations should certainly be one consideration."

In June, the City Council approved a letter from the city to VTA Chair Joe Pirzynski expressing its interest in having the agency "update the representation structure" of the Caltrain board to "more accurately reflect ridership levels." The council requested that one of the three seats be designated for the four cities in the north county that make up Group 2.

"Specifically, the City is concerned that there is no Palo Alto representation on the PCJPB, despite having the highest ridership in Santa Clara County and the second busiest station on the entire Caltrain line," the letter signed by Scharff states. "In fact, there is no representation for Santa Clara County north of San Jose, despite over 75 percent of Santa Clara County boardings being north of San Jose."

Any change to the VTA's appointment policy will have to wait until January. Pirzynski noted in a July letter to Mountain View, which submitted a request similar to Palo Alto's, that the decision about Caltrain appointments is made at the beginning of each year by the incoming board chair (in this case, it will be Ash Kalra, Price said).

The Joint Powers Board board made an overture to the underrepresented cities in fall of 2012, when it created the Caltrain Local Policy Maker Group, an advisory panel that includes representatives from each city on the line. The City Council's letter noted that this is a "positive development," though members quickly pointed out that this role still doesn't give the city an opportunity to be directly involved in policymaking. In an April meeting of the council's Rail Committee, Councilman Pat Burt spoke for the entire group when he said: "We want to focus on getting a member on the agency that makes the decision, not just gives advice."

Getting Palo Alto a seat on the board could, however, prove to be an uphill battle. Kniss, who joined the Caltrain board in 2010, when she was a supervisor, said she had to wait 10 years for the opportunity. Palo Alto council members, who are restricted by the City Charter to two, four-year terms, don't have the luxury of waiting that long. More often, these seats are snagged by longtime politicians who don't have to worry about term limits. Kniss cited the example of Don Gage, a moderate Republican from Gilroy who joined the board of supervisors in 1997 and who subsequently spent more than a decade on the VTA and Caltrain boards.

Long terms on coveted boards have historically been the norm, Kniss said. Before 1991, the county board had no term limits (currently there's a three-term restriction), and it wasn't unusual for a member to serve for 20 years, Kniss said. She noted the example of Pirzynski, who in addition to chairing the VTA board also now serves on the MTC.

"He's waited long enough and been around long enough, so he gets to do it," Kniss said.

The recent proposal by Kniss, Shepherd and Price to extend the number of allowed terms for Palo Alto council members from two to three aims to make Palo Alto more competitive in these leadership roles. The June colleagues memo, which the council briefly discussed but did not take any action on, argues that the two-term limit in Palo Alto hinders the city's representatives from getting ahead on regional boards.

"Palo Alto council members serve on regional planning and regulatory bodies with complex responsibilities, for example preserving the Bay, countywide public transit, regional water planning, gas/electric regulation, ABAG, VTA, Caltrain and more," the memo states. "To effectively represent Palo Alto's interests, the city's representatives need time to gain expertise and build seniority on these bodies. Term limits interrupt this process."

In June, Shepherd made the case to her colleagues.

"Cities like ours that have term limits just never rise to the top in order to help work through some of the major policy issues that are facing cities of our sizes," Shepherd said. "I think this would be an important move for Palo Alto."

The council agreed that the idea is worth discussing but noted that it would require extensive community outreach and feedback from residents.

An enthusiasm for looking beyond the city's borders is one of the hallmarks of the current council, but this hasn't always been the case, Price said.

"Historically, depending on who is on the council and what their availability and expertise is, it has gone up and down," Price said, referring to council members' participation on regional agencies. "It sort of ebbs and flows."

Today, it's flowing hard, both because of the multitude of regional pressures and the hands-on nature of the current council.

"It seems now there's a confluence of many issues all at once, where it's even more important for cities to get engaged," Price said.

In a recent interview, City Manager James Keene wondered whether the inherent difficulties of getting involved on regional boards had prompted past council members to simply give up. When it comes to getting a seat at the regional table, Palo Alto is hampered both by its size and, possibly, by geography, Keene said.

"It's just conjecture, but I actually think our location is a little challenging," Keene said. "We're in Santa Clara County, but we're right in the northern end, and to that extent we're treated as an outlier within the county. On the other hand, we have lots of affinity with San Mateo County on issues."

For example, Palo Alto's primary partners are often cities like Menlo Park and East Palo Alto. The San Francisquito Creek Joint Powers Authority, which is charged with boosting flood control around the volatile creek, includes elected officials from the three cities, along with representatives from the two counties through which the creek runs.

This geographic predicament helps explain the city's ongoing battle with ABAG, the regional agency that doles out housing mandates to each city on the assumption that cities with a wealth of jobs should also provide more housing to reduce traffic congestion. As a result, the agency has called for Palo Alto to plan for 2,860 new housing units over the next decade, a number that city officials described in a letter earlier this year as "highly unrealistic and excessive." Palo Alto has been fighting these mandates for years, but the only concession it's been able to wrest from ABAG was an agreement earlier this year to transfer 350 from the city's allocation to Santa Clara County's. Here, the county line matters. While Palo Alto has been a lonely and frustrated island, its neighbors in San Mateo County have formed a "subregion" that allows them to pool their problems and offer a regional solution to their county's housing allocation.

Regional mandates have also created problems within Palo Alto. The public furor over the council's decision in June to rezone a site on Maybell Avenue to enable a 60-unit housing complex for low-income seniors and 12 single-family homes first manifested itself during a May meeting of the council's Regional Housing Mandate Committee. Residents protested the committee's inclusion of the 60-unit complex in the city's overall plan for increasing housing even before the Maybell project went through public review and approval.

Much like in the case of high-speed rail, local residents get angry when an outside organization dictates policies that would have a huge impact on the city — in this case, increased building density. This anger, along with specific concerns about traffic, helped fuel a grassroots campaign that led to Measure D, a citywide vote on Nov. 5 that will either sustain or discard the council's June approval of the Maybell project.

"Because the City Council is looking to satisfy an ABAG requirement, they're willing to set aside the Comprehensive Plan and the promises that were made to the residents and offer lots of different deals," Cheryl Lilienstein, one of the leaders of the "No on D" campaign, told the Weekly during a recent interview.

So far, the council's efforts to influence ABAG have borne little fruit. While Councilman Greg Schmid serves on the agency's General Assembly, which includes more than 100 people representing every jurisdiction, the city doesn't have a single representative on any ABAG subcommittee. Scharff, who serves as an alternate on the agency's executive committee, was one of the few elected officials to vote against the "One Bay Area" plan, an ambitious land-use document that was developed by ABAG and the MTC. The document represents the region's response to Senate Bill 375, a landmark 2008 law that calls for a 15 percent reduction in greenhouse-gas emissions by 2035. The plan forecasts that Palo Alto would need to increase its housing stock by 30 percent by 2040, a tall task for a council that often refers to its city as "built out." Scharff acknowledged that in his ABAG role, he has "no real influence."

"I have tried to give Palo Alto a voice, but without a seat on the board, it's virtually impossible," Scharff said.

Few on the current council have been as enthusiastic about looking beyond the city's borders as Nancy Shepherd. Last week, the vice mayor took her second recent trip to China. She was there for the Smart City Symposium, a conference that also included Oakland Mayor Jean Quan, Bay Area Council CEO Jim Wunderman and staff from Gov. Jerry Brown's office and from various regional boards.

The big theme is greenhouse-gas (GHG) reduction. While the issue is complex, Shepherd's mission is relatively simple. In an email from China, she said she is "making friends and telling the Palo Alto story about our contribution to the global economy and the successful efforts we make to reduce GHG emissions," which includes the council's decision earlier this year to make the city's entire electric portfolio carbon neutral.

Shepherd, like her council colleagues, sees many benefits in conferences of this sort. For one, they give council members perspective about Palo Alto's problems and allow them to talk to other mayors about possible solutions. At a recent League of California Cities convention, for instance, she was approached by a council member from Stockton who said he wanted to replicate Palo Alto's "Smart City Partnership" program — a recently adopted collaboration between the city and Yangpu District in Shanghai, China. Stockton, which is just emerging from bankruptcy, is trying to attract more port business and sees value in a partnership with China.

She was also pleased to hear about Yangpu's efforts to replicate Palo Alto's downtown thoroughfare, University Avenue, by developing its own street of the same name. Most California cities, she said, would gladly trade places with Palo Alto and inherit its problems, which mostly stem from economic success.

In recent months, Shepherd and Kniss have also taken trips to Kansas City for a conference on "fiber to the premise," a fiber-optics project that has been eluding Palo Alto for decades but that remains high on the city's agenda; and to Contra Costa, to learn about the city's transit district and its effective "transportation-demand management" program.

Making friends beyond the city's border also gives the city a leg up when it comes to funding, said Kniss. For one, it allows the city to know what types of funding sources are available. Kniss said sources at the county and the VTA regularly notify her about grants that Palo Alto may be eligible for. In fact, Shepherd called her from China to tell her about a transportation grant that is now available. She learned about it from Jack Broadbent, CEO of the Bay Area Air Quality Management District, who was also at the symposium and whose board administers the grant.

"My experience is that the more you get involved in your region, the more influence you're going to have and the more opportunities you're going to have, especially for finding out about the kinds of funding that doesn't come to every city equally," Kniss said.

Involvement in state, regional and national issues also allows local officials to make inroads with the people who distribute the funding. As a longtime representative of Palo Alto and the county, Kniss said she has benefited from her relationships in Washington, D.C., which are key to securing earmarks for her constituents. She cited the adage: "In business, as in life, it's all about relationships."

"If I walk into an agency in DC now and I know the people, who do you think they'll look more kindly at — the person who's been around for a while or the one who has just walked in for the first time?"

Keene is also a true believer in cultivating relationships and building partnerships beyond the border. His prior positions include stints as executive director of the California State Association of Counties and, more recently, as director of strategic issues for the International City and County Management Association, which includes about 400 cities and counties. In a recent interview, he cited Bruce Katz, vice president of Brookings Institution, whose recent book "The Metropolitan Revolution" makes a case that cities (as opposed to states or the federal government) are "the engines of change and social transformation in the United States." He also cited a recent report from Joint Venture Silicon Valley, which advocates for a stronger regional decision-making authority and argues that this can happen only through a bottom-up effort, rather than through mandates from the top.

The most recent Index of Silicon Valley, a joint publication of Joint Venture Silicon Valley and Silicon Valley Community Foundation, makes an argument that "some of the biggest threats to the Bay Area's long-term economic competitiveness are challenges best addressed through stronger or more effective regional governance." The report specifically points to the challenges of limited housing, highway congestion and the Valley's transit system, which is made up of 27 individual operators and dozens of different fares.

"While many of the Bay Area's 100-plus local cities and nine counties are trying to respond to these important issues, they are not capable of solving them alone," the 2013 index states. "Quite simply, jobs, housing, transit and climate change are regional challenges. By definition, regional issues require regional solutions."

Keene shares this view. He pointed to issues like sea-level rise and traffic and argued that the only way Palo Alto can successfully tackle them is to look beyond its borders.

"The complexity of the problems we're facing is just forcing us to rely on regional solutions as much as possible," Keene said. "Given the difficulties and, in many ways, the break downs at the state and national levels, the ability for localities to come together is really important."

Chart: Palo Alto's regional representation