Genre-Killer: The reception and sales of this game, along with the tendency favoring cover-based games and the apparition of several free arcade FPS, were the last straw for commercial fast-paced shooters.
Vaporware: The Linux and Mac ports. Since it's release date, Epic Games stated time and time again that they had contracted Ryan "Icculus" Gordon (who created or at least took a part in the ports for these platforms of many other games, including past Unreal installments) to create the Linux and Mac ports of the game. Screenshots showed up, there were messages about the development, but it wasn't until December 2010 that it was confirmed that those ports will never happen. Couple this with Epic giving lower priority to a PC game (they were more involved in the next Gears of War games and Bulletstorm) and we have a sad cocktail.
There were going to be massive multiplayer battles which involved giant maps, multiple objectives, side missions, and up to 64 players. This mode was going to be called Conquest, and it was replaced by Warfare, a modernized version of Onslaught.
Malcolm was going to be playable at some point.
In a 2005 interview with Mike Capps, he told that players could command bots by voice and they will report back current situation. It never made into retail in that form.
Some teams from UT2004 were supposed to be here, but never appeared.
Earlier previews showed that the "Canister Gun" was planned to be ported over from UC2 as a Grenade Launcher/Mine Layer/Bio Rifle hybrid, but then they realized it was going to be super complicated implementing 2 different possible ammo types simultaneously on the same gun.
Some maps featured on pre-release screenshots never made into final game or were heavily altered:
One of the earliest known public demos was played on a map named DM-E3City. It featured Malcolm blasting its way through streets and completing objectives.
WAR-OnyxCoast was originally going to be much larger and featured interactive objects like destroyable terrain, seen from the UT2007 trailer.
CTF-SearchLight was going to be included in the retail version. It didn't made the cut, though it was released later as a free addon.
DM-CarbonFire had a ramp leading from Shock Rifle up to the catwalk, no pit with UDamage and Berserk, and a different skybox.
Working Title: Unreal Tournament 2007 (there was a trailer which had a logo with this entry) and Envy.