Wild Animal Park is for older kids as the animals roam huge enclosures. They have a couple good shows but it pales compared to the Zoo (Balboa Park) for the young ones. Hot, like 100+ F in the summer months.
Lego Land - it's just down the street from where I live. I think it's suited for kids under 10. Your kids sound the perfect age. My daughter is 9 and wouldn't be caught dead there
Sea World is still great. I highly recommend it plus it's a 5 minute drive (no highways) from your hotel.
Balboa Park is worthwhile and do the USS Midway. They have lots of interactive activities (flight simulators) and stuff to keep kids of all ages interested.
Best beach is at the foot of the Hotel Del on Coronado. Old Town is fun for lunch but avoid the very busy Old Town Mexican Cafe. Terrible food and the worst margarita in all of SoCal. Eat at Casa Guadalajara in Bazaar del Mundo square. From old town take the trolley to downtown. Shopping at the outdoor Horton Plaza will be enjoyed by the wife. Next door to that is the Gaslamp district (4th and 5th avenue) with tons of good restaurants and bars with live music.
La Jolla shores is a good daytime destination to access the beach and then post beach food/drinks in downtown La Jolla. Georges at the Cove on Prospect is a sure thing for good food though pricey. Their top level outdoor seating cafe is great for the kids and has tremendous views of the cove.
There are tons more things here. If you have specific questions don't hesitate to ask.