This is my last night in San Francisco and will be on the long trip home by Amtrak starting tomorrow (Sunday)
While the locals may complain about it for the most part public transportation in the Bay Area is quite good. The only drawback I can see is that you have many separate transportation agencies and transferring between them can be a little complicated. The systems have been working on a unified smartcard system but now it appears BART is going off on their own and it is unclear if the BART card will work on the other systems.
BART is showing its age ( now over 30 years old ) and the system is showing wear and tear especially on the rail cars. I did find the vending machines easy to use and trains came quickly when the real time signs said they would.
The MUNI system in San Francisco uses streetcars, trackless trolleys, buses and of course the famous cable cars. The buses on average are older than Boston but I never had to wait too long for one and they can climb the hills in this city. They also have real time info on some routes in the bus shelters which was quite helpful.
Overall I found getting around the area easy by public transportation.