We just moved from there this past November. Oh, it's soooo beautiful. Since we lived there I didn't have to stay in a Hotel, but I have some quick recommendations for things you should do while you're there.
First, at Sea World, don't miss the Pet's Rule show. I know, who goes to SW to see cats and dogs, but it's a great show. And despite the warnings, you really don't get wet in the bottom rows. Also, the night show's are the best! So stay for the shamu and sea lion shows, totally worth it. We had annual passes and still went twice a week when we could! Oh and before you stand in line at the Shipwreck Rapids attraction, you should know it's really short and not really worth the wait. Journey to Atlantis however, is a blast.
Oh, and I know you plan to hit the beach, we frequented La Jolla Shores. It's big, the water's fairly calm and there's plenty of lifeguards. If you want to see tide pools Ocean Beach has some neat ones. Oh, and you have to go to Children's Pool. The seals come right up on the beach and there's a walkway that jets out into the ocean so you can get a good look. Really neat. Go in the early evening. Also, Torrey Pines is a great beach if you want to avoid some of the tourists. We started going there once we were more familiar with SD.
Also, instead of the San Diego Zoo, most people actually prefer the Wild Animal Park.
In La Jolla, try the Birch Aquarium, there's always cool fish and in the summer they have some neat exhibits for the kids to try.
Oh, and go downtown! It's really neat. Plus the Star of India is right near there as well as Seaport Village. Oh, I miss it a little can you tell? Especially in this heat!
We did stay at the Embassy Suites in La Jolla when we were evacuated due to the fires. It's super expensive, but it's beautiful.(We got a discounted rate because we were evacuees) And UTC mall is right across the street. So, um, yeah, if you want any more ideas or have any questions email me. Have a great trip!