Now at least they've added BART and VTA. I tried generating a few test itineraries between the south and east bay, and the results look reasonable. Hopefully, they'll add CalTrain soon (I sure see a lot of Googlers on CalTrain).
How they'll handle itineray generation for the basically unscheduled, non-deterministic system that is the Muni (Schroedinger's Bus, anyone?) will be interesting to see.