Several expressways are proposed to be widened. You propose several grade separations on Caltrain, which will serve mainly to make automobile use easier in those areas. If anyone should be paid to ride BART, it should be walkers, bikers, and bus riders, not drivers. The same goes for the proposed Park and Ride Lots. Providing feeder bus service to BART would be vastly cheaper and environmentally preferable to expanding parking facilities.
Land is far too valuable to be used to house cars.
The only reason I can see is that you are trying to attract as many federal and state dollars as possible to the Bay Area. In your case, you are selling the Bay Area's health and environment, to make a few bucks.