Luckily for id, they've learned a lot about presentation in the last few years. The storytelling has improved greatly, being exposed slowly through the emails and voice logs recorded on PDAs that have been dropped by their now-dead owners. Your current affairs are kept up to date via radio communication, and the plot also contains some mysteries, such as the two gentlemen you chase through much of the game.
id has definitely taken cues from other games in the way matters are presented. Mix a bit of Half-Life and System Shock 2 and you've pretty much got the presentation down. Of course, the technology has changed so much, and id's done so much labor on the game that there's literally no comparison.
Despite being almost entirely indoors, the levels of Doom III feel more alive than any other game's. The lighting is certainly a major reason why, but it's actually the manual effort by the artists, animators and designers that makes the difference. Textures are of course re-used, but never did I feel like I ever saw the same texture twice. There's always a bit of shadow or a different light or a completely different texture next to it that makes the two textures blend together.
Furthermore, many parts of the levels are very animated. Machinery goes about its work, moving back and forth or up and down. On top of that, many times in the game monsters will be pounding at doors, bending them in or even breaking them, or breaking through windows. There are scripted sequences everywhere, so many that you don't feel they're scripted because they never stand out.
This isn't like the original Unreal where the first level contained the great lights-out sequence, and then nothing else happened with the levels through the rest of the game. It's not even like Half-Life where a scripted event was a rare, pleasant bonus. The levels and action in Doom III feel very alive because the scripting isn't a big deal.
Of course, all that simply highlights the fact how poorly the action is really done. It's almost beyond belief that at no time during development the team didn't stop and say "Wait, are we actually having monsters pop out from behind secret doors in walls? Wasn't this one of the lamer decisions back when we developed the original Doom?" It's not that the enemies come through the ventilation system - which they sometimes do - or are climbing above you and then drop down.
They're quite literally waiting for the player to pass by, setting off a scripted trigger, then their door opens automagically without noise and they shoot you in the back. OK, fine, you got me id, that was sneaky. Made me jump back in the seat and I needed to take a break just two hours into the game. After eight hours of that, however, the feeling of fear is replaced with irritation.
When I woke up to play the last part of the game, it wasn't only annoying, it was tedious and expected. Yes, the better surprises - and there are a few - could still surprise or scare you. However, that core "SURPRISE!" gameplay element was used ad nauseum.surprise! monster steps out behind you from a secret room!