When I had to commute into San Francisco from Berkeley a few years later, I took BART into the city, and didn't fare much better. While the trains were on time more often than not, there were way too many delays when we were en route. Since the underwater tunnel between Oakland and SF is a choke point - just two tracks - whenever there's a delay in there and you were behind it, it would take at least an extra 15 minutes to get us moving again. The BART strike from 2013 was also pretty bad for commuters.
I lived in New York and have been to Osaka, Japan many times, and I don't mind public transportation at all in those cities - they cover a lot more ground than the Bay Area, have plenty of trains and buses and aren't too affected by delays when it happens.