A friend said it best: San Diego is a day-time town. Lots of great active sports, beaches; all the cool stuff to do is during the day. The Bay Area is more a night time deal. All the best stuff to do is at night (shows, restaurants, pro sports).
I love both. San Diego is 1-2 degrees consistently warmer year round. More sun. I do miss a good Indian restaurant, but San Diego is more family-friendly IMHO. Don't think my politics mesh as well in the Bay Area as they did before I left in 1999.