I for the most part really like BART. Fairly on time, decently priced and can get you across the city super quick. Things that suck are, breakdowns involving the transbay tunnel that literally shutdown the city, high traffic times and not made its way completely around the bay. Kind of sucks getting to a Sharks game other than riding the bullet.
It needs to be funded, and not just barebones, but needs a crap ton of money thrown at it for a good number of years. Might take a decade or so of a crazy amount of work.
EDIT: Tech companies have kind of ruined the bay area. You can call me an old man on this one, but they have definitely left their mark and I am not sure what the future is for the area once those companies move away, disappear, whatever...
Also, Minneaplois rail is kind of terrible. I mean its a start and better than most of the midwest, but its slow and limited.