I would consider taking the trolley down to the border and/or out to the stadium. Just because--kids like trains.
Belmont Park is a great little place, but it likely will disappoint after DL and Legoland. September is the best month for the beach in SoCal. Balboa Park is a good option. As I mentioned above, there is much more to do there besides the zoo. There often are cultural events going on in addition to the permanent museums and parks.