Why not spend (a small fraction of) that money to improve Caltrain and service between Caltrain and the central valley in a different manner?
I'm not convinced that the current HSR project is the best way to do it, but I'm also not aware of any serious counterproposal -- and it's hard to even imagine one that wouldn't also be a huge, expensive undertaking with limitless opportunity for missed schedules, cost overruns and undue optimism.
Most criticism boils down to a "perfect is the enemy of the good" problem. Anything that isn't the most perfect possible solution from a given critic's viewpoint is attacked as a "boondoggle" while ignoring that opening up the corridor and making it easier to travel between SF, LA, and smaller cities in between will be a good thing (and that there's plenty of evidence for it in similar rail lines elsewhere).
(hint: some of the money is going to be used to improve existing transit systems!)