We also went to the Clearwater Aquarium last summer, and it's nothing like the Florida Aquarium (Tampa)-it's much smaller scale, very few not so well-maintained exhibits, but also a lot cheaper. The best thing at Clearwater was the Sealife Safari- a boat trip where a marine biologist is on board, and they "trawl" for fish, etc. then show and talk about what's been caught. Our kids loved it. Also you get to see dolphins if you're lucky.
Of the two, I'd definitely recommend the Florida Aquarium; but Clearwater's Sealife Safari boat trip was better the Dolphin Quest at the Florida Aquarium.