The new show at the Nautilus Theater, Odyssea, is a replacement for Cirque de la Mer. I must add that I liked Cirque better since it was much more lively with the well-known Peruvian comic/mime who headlined the show. It is a great place to take kids to cool down and take a brief rest.
I recommend that you just look at the show schedule the day you are there and pick the major ones like Shamu Adventure, Clyde and Seamore, Key West Dolphin Fest and Pets Ahoy! and work your way around the park. Pets Ahoy is in a smaller indoor theater and usually fills on the weekends during the earlier shows, so I would make sure that you do that earlier.
If there are kids involved, you need to keep their needs in mind.