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3D Realms considered doing a first person sidescroller game. Thankfully, this idea was scraped.
There's also "lameduke", an early beta of the game. Thank your lucky stars that they decided to rethink the entire game concept. A map (Derelict) survived the purge, though.
Action Forms was going to release a urban hunting game called Duke Nukem: Endangered Species, a spinoff of 3D. It was scrapped.
The Pig Cop was originally supposed to be able to hit the player with their Shotgun, but 3D Realms dropped the idea, since it was not working in the game. This concept was rescued later for Duke Nukem: Manhattan Project, which features the Pig Cops.
The developers planned many features that ended up being scrapped. Some of them are Dummied Out, and traces of them can be found in game data. Some planned features and concepts include laser sight, space suit, flashlight, multi-floor elevators, boss spaceship, scorpion-like tanks driven by Pig Cops etc.
As shown in old alpha and beta screenshots, the levels were originally more detailed than in the final game. A possible reason for the change is that the mappers had to simplify the design so that the game could be played on slower computers.