Just to say you were probably in the best areas for pubic transit than most of the other parts of California, there are several bus and rail services along the bay area. Learning which ones to pick can help improve your experience (which may not be the obvious ones).
A lot of the "helpful" apps and sites don't compare against taking a few minutes with a paper route map and a few timetable pamphlets...
I just had a thought: maybe having a point to point travel guide where people are able to submit various methods to achieve that route and then let folk vote/rate/review the methods (ala Amazon review, stars and comments). So, say you enter SJC to SFO and since that is somewhat popular route you might see a few different ways posted to get here, along with reviews of how those went following those ratings and comments on the methods; you see the good, bad, and from what is written you might have some clue of what's actually better.