To be honest, I was disappointed by the Atlanta Aquarium when I was there last year. The huge tank is incredible, but beyond that, I felt like there wasn't much variety, and that the number of exhibits was far less than other aquariums. Right now, my #1 is the Monterey Aquarium. The multi-story Kelp forest there, with critters that came in from the Ocean during their "water changes" is amazing. Baltimore is a close second too, although it's been awhile since I made it up there.
I really liked the Tampa Aquarium when I was there 7-8 years ago, but admittedly, I wasn't much into the aquarium hobby then, so I'd like to go back to see if that impression still stands.
Seattle's aquarium was just okay, but did have some interesting exhibits about salmon and other north-western specific exhibits. New Orleans wasn't bad either, but I visited it pre-Katrina, so I'm curious how it looks now.
I'll have to put Chattanooga on my agenda next time we visit family down in those parts. Same with the Shedd.