I don't think I'm going to take public transit in San Francisco ever again. They are missing:
* Speed - BART is relatively fast, all Muni is very slow
* Frequency - BART is low frequency, Muni is also low frequency
* Coverage - BART coverage in SF is limited, Muni coverage is reasonably extensive
* Reliability - BART unannounced delays and breakdowns were a frequent occurrence. Unlike Tube delays (which were also frequent) I could not route alternatively because there is only one BART tube in SF. Muni does not have arrival times.
* Usability - You cannot tell before you pass the turnstiles at a BART station whether the lines are delayed or when they will arrive. One exception I know if is Montgomery St. Station but that's the only one.