Compared to places like New York, Tokyo, Singapore and London, where everyone makes use of the transit system, in the Bay Area, only those who are impoverished would consider trying to get anywhere using bart + caltrain + public buses.
Everyone else (for reasonable definitions of "everyone" - there is obviously a small group of people who make use of bikes to work) either (A) Drives (majority), (B) Is lucky enough to have a place of work near a caltrain station (rare), (C) Has an employer provided shuttle to take them from Caltrain to their place of work, or (D) Uses a Company provided bus.
Compare this to a place like Singapore, where the MRT + buses are actually a very viable option to take you anywhere in the country.
I don't know how feasible or reasonable it would be to have an integrated Bus, Bart, Caltrain transit system, with easy connection/transfer from each stage would be, but, at the very least, cleaning up the Bus System so everyone felt comfortable using them would be a nice start.
I'm still hoping the various counties can get over their insecurity and eventually run BART around the bay one day.