EG, newtonsapple --
Thanks for the update; my experiences with the BART to SFO trip were right after its opening. Your more recent "smooth" experiences encourage my trying again.
Beyond that, I'll comment that BART was conceived as (and in fact is) an updated version of the old-fashion "interurban" train system. It's primary purpose is to move people from city to city within a region, not from neighborhood to neighborhood within a city. As such, user-friendliness of the system-to-system interchanges is vital to customer satisfaction. BART and the local transit agencies do reasonably well, but I'd still recommend that they take a good look at Paris RATP's interchanges between the RERs and Metro, which has been the best I've experienced.