With the regional push for a transportation tax measure cruising toward November 2016, Palo Alto, Mountain View and other cities in northern part of Santa Clara County are joining forces to make sure their needs don't get overshadowed by San Jose's.

The unusual alliance between 11 cities in the northern part of the county was prompted by years of complaints about the lack of balance in how the tax funds have historically been allocated.

According to an analysis by the office of Santa Clara County Supervisor Joe Simitian, whose district includes the northern part of the county, nearly 80 percent of the funds from the past two ballot measures have been spent on the extension of BART from the East Bay to San Jose. This includes the entire $320 million raised so far from the 2008 measure and $3.3 billion of the $4.3 billion raised from the 2000 measure.

Simitian's analysis also showed that District 5, which also includes a portion of West Valley, received just 5.3 percent of the proceeds from the 2000 measure. District 1, which includes the remainder of the West Valley cities, received just 4.5 percent from that measure.

Now, the cities see the 2016 transportation measure as the perfect opportunity to change that imbalance. To that end, elected officials and city managers from these cities have co-written a letter urging the Santa Clara Valley Transportation Authority (VTA) to consider more comprehensive and integrated transportation solutions that would serve the needs of the entire county. It calls for the VTA, the agency pursuing the 2016 measure, to initiate a comprehensive study to develop a "system-wide plan that integrates future mass transit investments in Santa Clara County with connections to other counties, via such systems as Caltrain, as well as community-level systems and 'first/last mile' strategies,'" the letter reads.

Though the letter doesn't specifically mention the proposed tax measure, its strategic significance is clear. With highway traffic around Palo Alto, Mountain View, Los Altos Hills and Cupertino severely congested during the morning and afternoon rush hours, officials are trying to ensure that a good chunk of the funds raised through the potential tax will help remedy the situation.

During a lengthy discussion that dominated its first meeting after the summer break, the Palo Alto City Council expressed its own frustrations about tax allocations and unanimously approved the letter to the VTA, which calls for the county to focus its attention on commuting patterns along busy Peninsula arteries such as U.S. Highway 101, Interstate 280, Highway 85 and State Route 237.

Signaling the renewed spirit of cooperation, Mountain View Mayor John McAlister and Councilman Lenny Siegel both attended the Palo Alto meeting. Siegel told the Palo Alto council that the root of the problem in Santa Clara County is that "we don't have a transit system in the county that serves our existing commuting patterns."

"A study of our transportation needs throughout the county and beyond is something that has to come out of the current process," Siegel said.

So far, the VTA's approach to the measure has consisted primarily of conducting surveys and soliciting projects from each city in the county. The process, known as Envision Silicon Valley, aims to collect all the data and then use it to figure out which projects to fund. With San Jose boasting the largest population in the county and the most representatives on both the VTA and the Board of Supervisors, the BART extension is expected to do well once again. Bike projects, bus programs and pothole repairs throughout the county are also expected to win allocations.

Palo Alto's top priority is Caltrain. On Monday night, the city reaffirmed its commitment to boosting Caltrain's capacity and moving the train tracks into a trench so that they would no longer intersect with local streets. The project, which would cost more than $500 million in the southern half of Palo Alto alone, is one of dozens the city is preparing to submit to the VTA -- a list that also includes bike boulevards, an expanded shuttle system and the potential widening of Page Mill Road.

In this crowded field of projects, the trenching of Caltrain stands out for its scale, cost and overwhelming popularity. Palo Alto's 4-mile rail corridor is expected to get busier in the coming years, thanks to Caltrain's electrification (which will enable an increase in trains) and the potential arrival of high-speed rail, further complicating the already inconvenient east-west journey in the southern half of the city. Recent clusters of teenager suicides on the tracks added urgency to the project, with officials now focusing on "means restriction" as part of the citywide suicide-prevention effort.

Lest the VTA miss the point, Palo Alto supplemented its laundry list of projects with a shorter priority list, which includes Caltrain in the top spot, followed by bicycle improvements; first- and last-mile services from Caltrain to employment centers in north Santa Clara County; and support for "transportation-demand-management" (TDM) policies, which shift commuters from cars to other modes of transportation.

Councilman Tom DuBois was one of several members to call trenching Caltrain his "one priority."

"I think it has an opportunity to improve Palo Alto in a way that no other option really offers," DuBois said, noting that train frequencies are set to rise in the near future.

The project would "improve quality of life" in the Peninsula cities, eliminate the train-safety issues and eliminate train noise, DuBois said.

"I think this is a time to start really asking for a large amount of money from the sales tax to be for the trench," DuBois said.

His colleagues agreed, though the vote on the priority list split 5-3, with Councilwoman Liz Kniss, Councilman Eric Filseth and Vice Mayor Greg Schmid voting no (Councilman Greg Scharff was absent). Though no one disputed prioritizing Caltrain, the dissenting members wanted to defer the full discussion about prioritization until next month, when the council is set to discuss the city's long-term vision for transportation. The full list, which includes about 50 projects, was approved by all eight council members.

Council members also unanimously agreed that Palo Alto should strengthen its collaboration with neighboring cities and lobby for a regional transportation plan. Filseth pointed to San Mateo County, which has a coordinated transportation plan, and argued that Santa Clara County should follow that model.

"The Envision Silicon Valley measure doesn't feel like that," Filseth said. "It feels like a single-point project wrapped around with a scaffold designed like a political poll (created) to pass a public vote."

Councilman Pat Burt, a long-time advocate for a Caltrain trench, thanked the Mountain View council members who attended the Monday meeting and said he is "very encouraged by the current Mountain View council's interest in working together with Palo Alto."

"We look forward to cooperating," Burt said.

Mayor Karen Holman, who took part in putting the letter together, said she anticipates more cooperation with neighboring cities in the coming months. She agreed with Filseth and Councilman Marc Berman that the process used by the VTA is "flawed."

"It focuses a lot on pothole repairs, which all the cities acknowledge is not going to solve any kind of major transportation issue," Holman said. "It's going to get someone to punch the card (on the ballot) but it's not going to solve the transportation issues."

But even with the greater cooperation, success in securing funding is far from certain. Palo Alto has no representatives on the VTA's 18-member board. And four of the five districts in Santa Clara County include sections of San Jose, making Simitian the lone voice representing the northern section of the county. Councilwoman Liz Kniss, a former county supervisor, warned her colleagues that the VTA is "dominated by San Jose."

"I sat there for the first two years desperately trying to get money into north county and away from BART -- it's extraordinarily difficult," Kniss said.