My problem with Doom 3 is that it wasn't Doom. It felt like a Doom mod for Half-Life, or maybe a Half-Life mod for Doom.
I think its an ok game, but even though I'm actually not that big of a Half-Life or HL2 fan (I know blasphemy, don't get me wrong, I understand why they are lauded but they just aren't my favorite for various reasons), I feel it aged a lot better and is by far a better game.
I didn't mind the flashlight bit, although I do think that's a valid criticism and they could have made it just as scary (battery? have to have filters to see in some conditions, stuff like that) without the weird limitation.
Doom 3 did some things really well, in fact, I kinda get the impression that it was quite ahead of its time in some ways graphically, but I also think that worked against it. The game models were a bit of a mess (the character/monster models especially although some were ok and the animations were a bit hit and miss) and the textures were bleh. It seems to me that many of the graphical things it did so well just don't matter that much (I believe shadows were really exceptional and it did some interesting things with lighting, but I think the "smoke and mirrors" with better models/textures of recent games offers a much better end result).
I don't want to fault id too much for not just making another sequel (for instance, the newest Serious Sam, its like the same old with better graphics and that's ok, but I'd prefer them to try and push things in some way, like Serious Sam would be amazing with tons of destructibility) as I get they wanted to do something different and make Doom much more of a scary game, I just don't think the end result was that impressive.
Ultimately Doom 3 didn't live up to expectations and I feel it is a poster child for how FPSes changed, and in my opinion, not for the better. I think what really hits the head on why I find the game so mediocre is comparing it to say Chronicles of Riddick that came out around the same time. I know they're quite a bit different gameplay wise so its not a great comparison, but Riddick seemed similar but better visually, much more interesting gameplay wise (and they allegedly scaled back the gameplay some). It was like, it took id how many years to make this?
Oh, and I'm utterly disappointed with the BFG version. Its like a somewhat improved version that comes nowhere close to some of the mods for the original game (Doom 3 I mean), which really helped give it back some of the feel of Doom. To me it should have been a much higher quality experience, with maybe a "classic" mode (or the earlier games in the D3 engine).