We stayed in San Diego for a couple of nights at the end of a work trip (trade show in Anaheim). We stayed in the Gas Lamp district at the Kimpton Solamar (dropped off our rental car at the airport on our way in to town - we needed it in anaheim and Escondido but not in San Diego). Our favorite outing was the USS Midway - we spent an entire morning there (they open at 9?) After, we walked to Ironsides (in Little Italy) for a late lunch - I had a half dozen oysters and octopus a la plancha, possibly the best octopus I've ever had.....
(we started the trip with 2 nights in Laguna Beach, which is why we stayed right in San Diego - we weren't looking for the beach experience)