The California HSR project is a conceptually flawed design that's basically laid out by "let's make a deal" strategies. Let's look at the pit stops on the first leg, starting at a San Francisco terminus:
This is not a high speed rail design, it's a Metrolink system (choo-choo train) at best; perhaps 4 hours transit under good conditions. This is a gerrymandered design by politicians, not engineers, which won't comply with the bond requirement to make the transit in 2.5 hours. HSR doesn't make pit stops, it's a very large machine that requires intensive engineering and very high maintenance on straight routes. Needless to say, it can't safely share tracks with regular rail, as is now proposed. The land has not been purchased yet, and many lawsuits are brewing over the "taking" of farmland, among many other issues, because the route cuts across acres of farmland, rather than paralleling the I-5.
The bids are questionable and costs are not reliable. The low bidder has not been found to perform on previous projects. Newspaper editorials recommend scuttling the project for these reasons. The Reason Foundation has issued a report for this design citing ballooning subsidies that haven't been financially thought through. It is, overall, a sad example of patronage.
The solution for an HSR system is to build out regional transit in SF area and LA area with light rail and busses, which can be accommodated with existing facilities, stations and routes. This is the more appropriate development of urban transportation systems. They all need to work together at the right scale, and the connection to the big HSR system can happen at the two end points, just as they do in European systems. The route should run adjacent to the I-5 highway which already has clear right-of-ways and grading.
Spare the taxpayers from this pork, the state's already broke.
Update 3/15/16: Calif. Sen. Dianne Feinstein’s husband wins CA rail contract
Update 10/3/16: Jerry Brown’s Train Wreck
Update 11/22/17: Another setback for the bullet train