We took the 'paid' tour which was a shuttle bus over to Atlantis plus a "tour" and then we were free to check out the Aquarium and the resort.
The issue was the total disorganization of the tour. I think we paid almost $100/pp and when we arrived, Atlantis sent us on a goose chase to get our 'bands' we needed to get access. They didn't bring anyone to us but gave us vague directions to walk and find it. There was a group of 6 of us and we had a baby with us. We walked the entire casino and got to the other side to find a group of youngsters who worked there who said that the person with bands had left.
So we burnt a good hour of the tour just 'waiting' and I found it to be a bad experience. Plus, the aquarium was really kinda sad and there weren't a ton of 'animals' to see and we ended up going back to the boat early and trying to get back to a better environment.
So personally I didn't feel like it was worth the hype and maybe if you are going to Atlantis to 'do' something like pay to swim or do the Dolphins it'd be different but just to 'see' it wasn't impressive. Felt like a cheaper version of any Vegas casino.