Originally, we wanted to fly into LA and out of San Diego, but we found the flights and rental car to be considerably more expensive when starting in one city and ending in another.
We ended up flying into LAX and rented a car through Budget. We got a great rate by booking early and using a code found on mousesavers.com.
We are DVC members, so we stayed at GCV for 3 nights (did DL, DCA, & beach those first few days).
Then we drove to San Diego (stopped at San Juan Capistrano mission on the way). We stayed at Best Western Plus Island Palms. It was nothing fancy, but it was clean, had two small pools, a decent restaurant, and beautiful views of the marina.
While in San Diego, we went to the zoo, the USS Midway, and some museums in Balboa Park. Our hotel was a short (less than 15 min) drive to each of these attractions.
We then drove back to Anaheim and checked back into GCV for a few more days, did Disney parks a couple more days as well as La Brea Tar Pits and some touristy Hollywood stuff.