Odd, I disliked Doom 3, but liked Prey, Doom 3 got too samey and I don't think the level design and plot design worked as well as it could to keep me happy, though I did complete it...with an ending I thought was rubbish.
But then, when somebody uses a plot in a game, then I expect it to be good and keep in consistency with the quality of the game (or better), not some generic stuff that a Doom fanboy could have come up with. I know somebody will say 'what about the PDAs?', they still don't stop it from being generic, it's just they've been a bit more creative about it.
However, Doom 3 did have some good features, it was certain areas that needed more attention and hopefully Doom 4 will pay attention those areas.
"Experience never provides its judgments with true or strict universality; but only (through induction) with assumed and comparative universality." - Immanuel Kant