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!)
Why not spend (a small fraction of) that money to improve Caltrain and service between Caltrain and the central valley in a different manner?