Wife and I just got back from San Diego. Beautiful place. If it weren't for the politics I'd consider living there.
We ended up staying out by Mission Valley. Very convenient location. We could get to most attractions in under 15 minutes and the hotel was a lot cheaper because it included parking, breakfast, and wifi for what the room alone would have cost us closer in. Plenty of restaurants and stores nearby. First night we went to Target and stocked up on snacks and bottled water.
For future San Diego visitors, here's a money saving tip. Get a Go City Card for San Diego attractions. We saved about $60 using the card rather than purchasing tickets at the gate. We visited Legoland (skip this if you're over 11), USS Midway, took the one hour harbor cruise, the old town trolley tour (gave us an idea where we wanted to go and where we didn't), visited Seaport Village (tourist trap), Birch Aquarium (disappointing), and took a walk on the beach near Encinitas. We drove through La Jolla. Interesting area but we couldn't find parking. After about 45 minutes we gave up and said we'd try again another day. Unfortunately we never made it back. Next time.
Thanks to everyone who made suggestions.