HI! I just moved to Gilbert from San Diego last November, and I miss it so much! I'm not sure where the Bahia is, since I never really had to stay in a hotel (except when we were evacuated because of the firestorm), but the Birch Aquarium (Scripps) is an inexpensive way to spend a few hours. Usually during the summer they have additional exhibits and interactive play for the kids as well. It's small, but has a ton of great ocean animals! You can even touch some of the creatures in the tide pool. My kids loved it.
Also, about Sea World, the night shows are AMAZING! Sea World is going to be really busy, so when you get there plan your day around the shows you want to see. You'll need to get to them at least twenty minutes (maybe more)early if you want to get a good seat. It's worth it to go in the morning, spend the better part of the day there, and then grab dinner outside of the park (the food there is expensive, and not great, with the exception of the smokehouse place and the deli in the Budweiser store) and then go back for the night shows. They have fireworks and Shamu rocks is so much fun! The Clyde and Seamore show (sea lions) is hilarious! Oh, and go to the Pets Rule show, it's so adorable, I know you don't go to Sea World to see dogs and cats, but it's worth it. We used to go twice a week to Sea World and we always had to see that show.
Also, there's a place called Belmont Park. It's not far from Sea World, and there's a boardwalk and a little amusement park there. There's some fun places to eat and get Hawaiian shave ice. Ocean beach is great for Tide Pools, and Children's Pool is free and neat for the kids to watch the seals and sea lions come up on the beach. be sure to go in the evening if you want to see them. And parking is horrible, so you may have to walk a little.
I noticed that you're doing a Harbor Tour, while you're downtown there's a cool ship called the Star of India that you can see, and Seaport Village is there. The gaslamp district is neat, but be careful of the one way streets! Since you'll be at the zoo, take a look at Balboa park, there's a lot to do there too.
Ok, sorry for all the run ons, I miss San Diego a little can you tell? This heat makes me really miss it! Have a great trip and feel free to contact me directly if you need any directions or further ideas. I know where all the cool malls are too!