In this case Mr. Mouse is not far off the original plan. Something near San Jose is in fact a necessary stop - perhaps, really, the appropriate north end of high speed running - and being part of the Bay Area it could be the point from which the 2 1/2 hours starts counting, since it makes the job much easier than timing from SF itself. But real life tends to move faster than major public works, so San Francisco is in fact an important stop now - a large chunk of the tech money has located there, which wasn't the case when the current HSR scheme was proposed. The Peninsula portion of HSR won't be able to stay a Caltrain express (perhaps stopping at Millbrae for a BART shuttle to SFO) forever if SF stays a tech hub and HSR market. And the Altamont alternative to Pacheco, while providing an inarguably useful transportation alternative with instant full commute loads (high speed ACE train, with a Fresno extension), would not serve San Jose as well as Pacheco for direct runs to LA.

The question at this late date is: do we really care anymore about a 2 1/2 hour express to LA in possible competition with air travel? If not (and the current route diversion via Palmdale suggests that it's not as important as is claimed), Altamont is worth another look for transportation utility as well as potentially lower construction cost than Pacheco. Fresno as a bedroom community for Silicon Valley would still work with an Altamont route, just as a slightly longer trip. And what's under construction in the Valley now would work with either Bay Area access route. Of course, for the same reason, keeping Palmdale as a stop is useful from a transportation standpoint, and provides a convenient point to connect to a Las Vegas branch aka Desert Xpress aka XpressWest. IOW, HSR as part of a transportation system, not a flyover shot between SJC and LA downtown (Hyperloop can do that, someday).