The most contentious technical issue about the California High-Speed Rail project is which alignment to use to get from the Central Valley to the Bay Area. The two options are Altamont Pass, roughly paralleling 580, and Pacheco Pass, much farther to the south. A summary of all alternatives can be found on page 115 of the revised Bay Area-Central Valley EIR. For more detailed examination of the alternatives, see the old EIR: the base Altamont option is on pages 903-4, the base Pacheco option on pp. 969-70. Although Altamont is somewhat longer, the two alignments are about even on travel time from Los Angeles to San Francisco (in fact, Altamont is 2 minutes faster).
The basic tradeoff is that Pacheco is somewhat faster for LA-San Jose and serves San Jose and San Francisco on one line, while Altamont is much faster for Bay Area-Sacramento and requires less construction overall and has separate branches to San Francisco and San Jose. Overall, Altamont is superior because of its advantage for travel from the Bay Area to Sacramento and the Upper Central Valley (except Merced, whose commute ties to the Bay Area are weaker than those of Modesto and Stockton). Transit activists and environmentalists either preferred Altamont or did not have an opinion. However, San Jose didn’t want to be left on what it perceived as merely a branch, and lobbied hard for Pacheco, and as a result Pacheco became the preferred alternative; in addition, unlike the NIMBYs on the Peninsula, the NIMBYs in Pleasanton and Tracy complained about HSR early.
A third option is to go via Altamont but enter San Francisco from Oakland via a second Transbay Tube (old EIR, pp. 957-8). The EIR projected it to have the highest ridership, since it serves both San Francisco and Oakland on one branch and has the shortest LA-SF travel time. It was rejected because a second tube would be very expensive, though in fact the EIR pegs the cost of this option at a few hundred million dollars more than the base Pacheco and Altamont options; urban construction along the Caltrain line is expensive as well. In a crunch trains could continue along an electrified but not otherwise upgraded Caltrain line at lower speed, reducing cost, but by a similar token people could transfer to BART at Livermore under any Altamont option and at West Oakland under a second tube option. However, should a second tube be built anyway to relieve the near-capacity BART tube, such an option would become far and away the best, making all others redundant.
The choice of Pacheco became one of the galvanizing features of the technicals in California, who without exception preferred Altamont. To answer concerns that Bay Area-Sacramento travel has to be served, both the HSR Authority and various politicals have proposed a cure that’s worse than the disease: build a high-speed commuter overlay along Altamont (the official version) or the I-80 corridor used by Capitol Corridor trains (consensus among pro-Pacheco blog commenters, see e.g. this map with a second tube just for SF-Sacramento trains).
Pacheco itself is mildly defensible. It would arguably have been superior if Sacramento did not exist, and I-80 would have been the better alignment for SF-Sacramento service if LA did not exist. But given that LA and Sacramento both exist, Altamont’s ability to serve LA, Sacramento, and SF with just one expensive bit through the pass becomes more valuable. If Altamont is built, there would be no point in a Pacheco overlay, whose primary use would then be a frankly uncompetitive connection to Monterey. But Pacheco leads to demands for an overlay service, one that’s almost certainly too expensive to build just for Bay Area-Sacramento travel.
The Capitol Corridor, the other option for SF-Sacramento service, is too slow. With a bus connection from SF to Emeryville, the fastest service takes 2:08 from downtown SF to Sacramento. Even Pacheco beats that: express trains detouring through Gilroy and Merced will nominally take 1:53; service via Altamont is a little more than an hour . For SJ-Sacramento travel, it’s 3:05 on Amtrak and 1:24 via Pacheco. Substantial upgrades are impossible since Union Pacific owns the track and restricts passenger trains’ performance in order to remove a headache for freight operations. The remaining option is to build passenger-dedicated bypasses, at considerable cost and with little benefit over doing it right the first time.