Yeah, SF proper will not go for elevated tracks, except in the south where BART is elevated. I wish they'd try a simpler solution for street level issues: giving trains the right of way. On the Embarcadero, the trains have to stop with the cars at stop lights; this makes little sense in my mind. The light should switch for the train like it's a firetruck.
As for underground, I believe they are considering changing the rules regarding bikes on the trains, I know I read this recently, but they won't fit during rush hour, that is for sure. Muni trains are so packed at peak hours that I have become accustomed to getting very, very cozy with my fellow San Franciscans every day. I don't mind really. I guess we could hire people like you see in Tokyo, that push the trains full, but I doubt we see that happen.
It sounds like more of the delays are from maintenance and traffic anyway. I would like to hear about Boston's maintenance problems with these trains, see what they are doing differently, if anything.
I think it boils down to the fact that a ton of people ride these trains, they have to deal with traffic, and it's not privately run like BART...which of course has it's pros and cons.
Long story short, it's not a great system, but I will pick it any day over driving in this city.
PS. Yes the F Train is the old style line you are thinking of. It's not as comfortable for sure, but it sort of makes up for it in old world style.