In defense of the use of the Quake 3 engine for Doom 3, Jim Dose, one of the leading programmers claimed that the engine will be stripped and rewritten string by string.
In reply to eager gamers, Jim Dose claims that there are new things to be expected of the engine, in the words of the man himself:
" The engine is being completely rewritten, just piece-by-piece. Currently, the renderer, shader system, and game code are completely new. The cgame and network code have been removed. The animation system is currently being written from the ground up. The sound system and UI are still in place, but will be rewritten by Graeme and Robert when they are finished with the mission pack. At some point along the way, John will probably write a new network system.
So, even though we are not starting out with a blank sheet of paper, the final result will be a full rewrite."