SF is actually one of my favorite cities on the west coast. Many diverse and interesting neighborhoods, all blanketed by the feel of San Francisco. Fisherman's wharf is interesting in its own right, but I too try to avoid it. It is fun to people watch a little.
They are in the process of extending BART to SFO, but it isn't something that is going to happen overnight. I seem to remember 2003, but it might be scheduled before that. In the meantime, go upstairs and straight out, and you will see the blue shuttles. Only about 10 bucks or so, but they take a few minutes more.