Within the game's data are unused voice clips for a solo boss fight against Professor Calamitous, who in the released game only appears during the final battle against the full Syndicate. Some of these clips feature Calamitous threatening to destroy Retroville with a doomsday device, a subplot not present in the final game. This implies that Jimmy Neutron's route was originally going to follow the same formula as Danny Phantom, SpongeBob SquarePants, and Timmy Turner's routes, in which the team visits an individual character's world and foils a villainous scheme by an individual member of the Syndicate there. This is corroborated by a pre-release screenshot in which the monochrome Retroville simulation seen in "Fantastic Voyage of Goddard" is instead in full color.

There were initially plans for an Xbox version of the game to be released; however, it ended up being cancelled for unknown reasons. A relic of this is present on the game's IGN page, which still includes the Xbox on the list of platforms as of March 2024.