With a transportation-tax measure speeding toward the November 2016 ballot, cities throughout Santa Clara County have collectively submitted more than 600 projects that they'd like to see funded with the new tax. But while recent polls show strong support for the measure countywide, many in Palo Alto remain highly skeptical about any proposal that does not separate the train tracks that serve Caltrain from city roadways.

The City Council on Tuesday night made a fresh case for why such an ambitious and potentially transformative project should be at least partially funded by the measure, which would raise the sales tax by 1/2 cent and would raise about $6 billion for rail, expressway and road-repair projects throughout the county.

And after hearing the latest update on the tax measure from Carl Guardino, CEO of Silicon Valley Leadership Group, council members took turns making the case for a so-called "grade separation," which would involve building a trench for Caltrain. The project would have an estimated price tag of about $1 billion.

Guardino, whose business group is leading the drive toward the tax measure, had plenty of good news to report about the latest polling numbers. In the latest survey by pollster Jim Moore, 73 percent of respondents said they would support a 1/4-cent tax increase for transportation, while 68 percent they would support a 1/2-cent hike. Guardino said his organization supports the greater increase.

"It's the view of the Leadership Group that if we're going to collectively do anything together in 2016, let's go big or not do anything," Guardino said.

The high polling numbers, driven by a thriving economy and rising traffic congestion, offered high hopes to proponents of the measure. Even more encouragingly, every category of transportation improvements proposed to voters won overwhelming support. According to the poll, 86 percent favored using the tax funds to finish the BART extension to downtown San Jose and Santa Clara; 88 percent supported fixing potholes and maintaining streets; 80 percent supported traffic-relief measures on county expressways (including Foothill and Oregon expressways in Palo Alto); and 84 percent favored improving bike and pedestrian safety near schools.

Caltrain also scored well, winning a 73 percent favorable rating (16 percent opposed using the funding for Caltrain while 11 percent had no opinion). But for Palo Alto, which is bisected by the tracks, no project is more important, city officials argued Tuesday.

Councilman Pat Burt said that the combination of a modernized Caltrain and the proposed high-speed rail system would bring more trains to the Peninsula, to the tune of one train every three minutes. This will happen on rail-roadway intersections that Burt said are "already at virtual gridlock."

"This is what a lot of my colleagues have been really focusing on," Burt said. "On the horizon, we don't have a choice or a preference for grade separation. It's a necessity. And if we don't have it, we're going to choke off the cities that are the crown jewels of the valley and destroy not only our communities but our economies."

Councilman Eric Filseth didn't dispute that extending BART is an important project but painted a similarly grim picture of the Peninsula's future without the trenching of the rail line.

With train frequency on the rise and high-speed rail planning to share the tracks with Caltrain by 2029, traffic conditions will deteriorate further, he said.

"Congestion is going to lobotomize the Peninsula into two long, thin cities," Filseth said.

While traffic flow is one concern, safety is another. Just two days before Guardino's presentation, a northbound train smashed into an unoccupied car on a south Palo Alto grade crossing. The tracks have also been the scene of two separate clusters of teen deaths by suicide since 2009, prompting renewed calls for submerging the rail line as a strategy for restricting people's access to the tracks.

Yet when it comes to upgrading Caltrain, recent tax measures have not gone as far as needed, council members argued. According to an analysis by Santa Clara County Supervisor Joe Simitian, about 80 percent of the tax funds from the last two tax measures have gone to San Jose for the upgrade of BART, a project with regional significance but little relevance for most Palo Alto residents and commuters.

This trend, which is reflected in Simitian's report, has made some Palo Alto residents and city officials skeptical about the new tax measure. David Coale, a member of the local groups Carbon Free Palo Alto and Bike Palo Alto, is among them. Addressing the council, Coale summarized his position with the idiom, "Fool me once, shame on you, fool me twice, shame on me."

"Since Measure A passed in 2000, 15 years ago, over 80 percent of our transportation dollars have gone to BART and we have not yet moved one person with this system on the Peninsula," Coale said. "In the meantime, Caltrain, which is the main rail system in the county, is over capacity and in serious need of upgrading."

The recent tendency of tax funds going mainly to south county for BART improvements has also prompted concerns among city officials in the north county and West Valley about VTA's process of soliciting and selecting projects that would be funded by the measure.

Last month, mayors of nine cities co-signed letter to the VTA calling for a comprehensive study to develop a "system-wide plan that integrates future mass 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 coalition, which also includes Mountain View, Los Altos, Los Altos Hills, Sunnyvale, Campbell, Cupertino, Los Gatos and Saratoga, argued that the study should begin as soon as possible so that it can "inform near-term project funding decisions."

In response, the VTA officials agreed to initiate such a study but made it clear that the study would not be used to consider projects for the current tax measure. In a letter to the mayors, VTA board chair Perry Woodward, wrote that he does not agree that waiting for a study to inform near-term decision is a desirable approach.

"As you know, it takes time to accomplish the objectives of these types of studies," Woodward's letter states. "Major investment studies can in some cases, take two or more years to complete. While a comprehensive, major investment study will certainly inform decision making for future projects, our regional needs are immediate and continuous. We don't have the luxury of a pause while we consider future options."

Mayor Karen Holman on Tuesday called the VTA's response letter "disappointing," while Councilman Tom Dubois echoed some of the public concerns about the unequal distribution of transportation funding.

"We haven't seen a lot of benefit from previous two tax measures," DuBois said. "There's serious questions on whether there is support for another sales tax."

Even so, the council stopped short of issuing any ultimatums or conditioning the city's support on the Caltrain's grade separation. Councilman Marc Berman pointed out that no one is denying the importance of finishing the BART project, but noted that Palo Alto and other cities on the Peninsula suffer from "pretty massive congestion."

"Those are challenges that cost more to fix that the funding currently identified," Berman said. "We are very realistic about the fact that this tax measure will not fully fund the problems that currently exist, but I think we do hope and even anticipate that it will be a very important piece to that bigger puzzle."

Guardino stressed that his group supports including Caltrain improvements as part of the package and spreading out the funding in an equitable way across the county's 15 cities and towns. He also told the council that his group would support putting a cap on how much of the funding would be spent on the BART project, possibly at 25 percent. He had made a similar commitment two weeks ago at a meeting of the Santa Clara County Board of Supervisors, upon request by Simitian, Guardino said.

"We need traffic relief throughout the county, not one portion of the county," Guardino said.

With a collective price tag of about $900 million, Palo Alto's list of 23 projects is relatively modest by comparison with other jurisdictions, Guardino said. Gilroy, for instance, had a list that totaled $1.9 billion, Guardino said.

"They have twice the need, or twice the appetite or twice the imagination that you do," Guardino quipped.

But while the Leadership Group supports Caltrain improvements, it's not clear whether this includes grade separation. Guardino noted that the list of projects submitted by the cities totals about $50 billion, far more than the $6 billion that the tax measure would raise.

And the polling question didn't ask respondents about grade separation but about "improving Caltrain commuter rail service from Gilroy to Palo Alto." What exactly that means is a question that several council members are hoping to see answered in the months ahead.