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Several things changed during the game's 3 year development period. Previews stated that your character would run the risk of turning into a mutant himself. You'd have to find antidotes to stop yourself from going completely insane. Also, you could gain superhuman powers that could be used to your advantage.

Early builds featured additional gameplay elements, like the ability to hide bodies (for more of a stealth-based style?). There was talk of boss battles with adaptive AI, and a general focus on AI over scripting.

A few enemies didn't make the final cut including an imposing-looking butcher (who can be seen in screenshots and trailers). A brief look at the game's files suggests that all the assets for these enemies are still there... but they don't appear in any levels.

Two weapons (a heavy machine-gun and a 'stick bomb' style hand-grenade) don't appear in the game but are accessible via console commands.