A crossover with Gargoyles was planned, but never made. Disney had been planning to make a series out of the movie, but turned it into a direct-to-video when it underperformed at the box office. This is also true with the future of this film's merchandise: To date, the only characters from the film that still appear in the merchandise are for some reason, Rourke and Helga.
The submarine ride at Disneyland was originally going to be based off this film, but the film's failure resulted in that ride being based off Finding Nemo instead. However, there is a restaurant at Castaway Cay called Cookie's BBQ, and part of Port Discovery's background music at Tokyo Disney Sea is taken from this movie.
Jim Hill has an article that goes on in length about things that were cut from the movie, which includes deleted scenes of the Squid Bats and Lava Whales. There was also a plan, very early in production, for a magician character, Zoltan the Magnificent.
A behind-the-scenes footage found on the DVD release and one of the tie-in games shows the original intro was of a group of vikings searching for Atlantis only to be attacked by a sea monster while engulfed in a storm, fully animated, voiced and with sound effects. While mystifying, the executives felt no connection nor desire to learn more about the city or its inhabitants so the intro was done over.