Been to both and prefer SFO. It gets cold at night with the wind coming off the bay, but it's nice during the day. If you decide to rent a car, there are lots of things to outside of the city as well, though you do not need a car in the city.
Also, if you do go to San Diego, my favorite thing to do is to sit out on the patio of the Hotel del Coronado with a nice drink and watch the Navy jets and choppers fly in from offshore.