During its drawn-out three year development cycle, Earthworm Jim 3D changed publishers several times. This caused some problems as the game was based on the Earthworm Jim TV series which by the time of release, had been off the air for over 3 years. Also many locations displayed in early versions of the game are nowhere to be found in the released copy (such as a level set in a house, where Jim is ant-sized), and locations that were kept from early screenshots changed drastically before release.
In some cases, entire characters were changed – originally, Evil the Cat was to be the boss of Fear, but was changed to Professor Monkey-For-A-Head at the last moment, although his face can be seen on the records and record needles in the level “Boogie Nights of the Living Dead”. Additionally, Evil Jim, Earthworm Jim’s evil twin from the TV series, was reportedly a part of the game. Early screenshots also display Jim riding his Pocket Rocket. The characters of Earthworm Jim had to be redesigned for the shift to 3D. When the game was almost three quarters done, it suffered from framerate problems and poor animation. [Info from Wikipedia]
Also Makubeku noticed that the eye window its squared on the beta instead of how it was on the final! A beta demo was found by Nes World (as you can see in the video below), but we are not sure how many differences are in there.
Thanks to Lucas Araujo for the contribution!