Unfortunately, the California High Speed Rail Authority, a state agency charged with planning the railway, will likely just be a historical footnote when the trains are finally running.
Although Schwarzenegger has tried to kill it, or at best put it on a starvation budget, what really seems likely to be the end of this project is the agency's own strange inability to settle on a route.
Two routes have been proposed to connect the Bay Area to the Central valley, one over the Pacheco pass (Gilroy to Los Banos) and one via the Altamont (Fremont to Livermore to Stockton). There are a lot pros and cons to both. The major pros for the Altamont route are that it will serve thousands more people (unless HSR itself triggers massinve new suburban sprawl near Los Banos) and doubles as a useful route to Sacramento. The pro for the Pacheco route are that it makes travel times from San Jose to Los Angeles several minutes quicker.
Both routes also have engineering challenges and environmental impacts, but although proponents of each route like to bring up these issues up when looking for flaws in the other, there's no clear winner in either of these areas.
In building anything, there will be design tradeoffs like this. Sometimes the decision is hard, but in this case I think it's easy: the fact that the Altamont serves more people both makes it a better route and makes the whole project more likely to actually happen: people in places like Livermore, Stockton, and Sacramento are going to have to help pay for it (estimated cost, $30 billion+), and they're only going to vote for it if they can forsee getting some use out of it.
Unfortunately, the HSR project has been in the hands of folks from the south bay who have got it into their heads that anything other than the Pacheco alignment is a huge civic snub to San Jose--Pacheco makes it a "hub", and Altamont a mere "spur". These are the same geniuses who planned the VTA's light rail system (which, while I will admit to having grown somewhat fond of it over the years, still remains the nation's least successful light rail system by far--which almost certainly also makes it the world's least successful one). They even went to the extent of arbitrarily dropping the Altamont route from consideration in the project's initial EIR--if you don't study it, you can't build it!
The MTC has now brokered a compromise of sorts--build both routes. Really. You seriously want to go to the voters, and ask them to pay for a $30 billion project which is now going to cost $40 billion because you just couldn't make a decision? Convincing voters to pay for this project was always a longshot--I think now it'd be for the best just to let the Gov cancel it, so the CA HSR can turn off the lights and call it quits.
This is not really such a bad thing. What our state should be focusing on now is incremental improvements to the speed, reliability, and interconnectivity of the rail network we already have (although it is so fractured it's hard to even see as a network). Imagine if CalTrain, BART, ACE, Metrolink and Amtrak all worked well, and worked well together. Imagine if we filled in a few gaps, and started stringing services together, and ran trains at easily achievable speeds, if not bullet train speeds. Shouldn't we try running trains at 100mph before 200mph?
Interestingly, the route proposed for HSR (Altamont) is almost covered by a patchwork of passenger trains already, with the gaps likely to be closed--CalTrain from SF to mid-peninsula, Dumbarton Rail to Fremont, ACE from Fremont to Stockton, Amtrak San Joaquins from Stockton to Bakersfield ... here there's a bit of a gap, though freight tracks bridge it via Tehachapi ... Metrolink from Lancaster to LA.
Suppose there was one through train, with a running time of, say, 6 hours. Would you ride it? I would. Sure, it's not competitive with flying for speed, but it beats driving, and I think there's a market there. I'm sure residents of the Central Valley would find a 2-3 hour train ride to the coast attractive. This is something that could actually be built, probably for an amount of money that state voters would give a thumbs up to without blinking (low billions, perhaps?). And once this is built, and running well--that's the time to ask for the big bucks for bullet trains.