The Monterey Bay Aquarium is the best Aquarium in California, in my opinion. But, that's in northern California..
Aquarium of the Pacific in Long Beach, CA is really nice. Pretty big, has walk through tunnels, feedings throughout, you can pet sharks, stingrays, star fish and anemones. Has a bird house where you can feed parrots from your hand. It has some absolutely huge tanks to filled with all kinds of sea life. It also has a big jelly fish section and a big sea horse section. This is probably your best bet in so cal.