What would I change about Doom 3? Very little. Maybe some AI/enemy behavior mechanic tweaks to make the combat a little more fluid and fun. To ignore the incredible artistic achievement that this game brought to the table by changing everything from the lighting, to the sound and music, to the character and monster designs, would be intolerably tasteless.
It is clear that id's artists took their time with the technology and really understood how to make a scene stunningly beautiful with the then-incredible technology they got to use. The lighting in this game is still unmatched, to me, not in terms of realism or technical prowess(where it is easily trounced by several modern games), but in terms of style. The game's ability to bring out an absolutely beautiful scene in a room really does remain unmatched, I think. Turn on the lights, as some have suggested? Go fuck yourself and play DNF. Furthermore, some of the architecture and character gear designs were so good, I'd say they're reminiscent of some of the greatest designers in visual entertainment ever. Thinking specifically of Mobius. They furthered this taste in design in some of Rage's characters.
As for the gameplay? No, sorry, the game isn't an action game. It is a horror game. But, as previously mentioned, the gameplay isn't at all beyond criticism. I think some enemies are downright annoying to kill, and just aren't fun to fight. Again, this is something I think they pretty much nailed with Rage.
These things are mere tweaking problems, up against "OH LET'S GET A CHAINSAW ARM," or, "TURN ON THE LIGHTS AND CRANK UP THE METAL MUSIC MUURRRRR." Even the "I want 50 enemies" suggestion misses the point. Can you imagine having 20 (or whatever other arbitrary DOOM 1-ish number you want) Doom 3 imps on you at once? What a gameplay clusterfuck. The problem isn't the number, it's the mechanics of how the monsters behave.
The Doom 3 forum never ceases to astound me with its never-ending flow of moronic posts featuring terrible, almost senseless alternative game design suggestions. Oh, and the re-hashing of threads that have existed for years, and years... and years. It happens nearly daily.