I asked this question at one session and am not sure I really got an answer.
There seem to be two types of barriers to making transit in the Bay Area more usable: technological (operations) and political. There are no end to the technological solutions that are already being put into effect (NextBus, 511.org, improved rail and bus technology, BRT, better ways to collect fares, jiggering with transit routes and schedules, etc. etc...), however, the 800 pound gorilla is the fact that we have 36 different and sometimes antagonistic transit systems blanketing the Bay Area. Greater Boston, with a similar population and area and variety of modes of travel (bus, trolley, light and heavy rail, even ferry boats!, and far too many cars for the amount of highways), has one (1!!!) system, the Massachusetts Bay Transit Authority. It's not perfect, by any means, but seems to work a lot better than here.
Far too often, reasonable technological improvements become impossible because of agency posturing, turf protecting, struggling over the dollars that are available, etc.
How do we overcome this gorilla of politics that effectively blocks many of the technological ideas that so many of us were coming up with last weekend?