Definitely Doom 3. I grew to love Quake 4 by the end but, for whatever reason, for the first like 6 hours there aren't tons of enemies, your squadmates kill the atmosphere, and it's just pretty boring. It does pick up and feel more like Quake II for the last 12 plus hours, but Doom 3 is solid throughout. Whichever you choose, make sure to play on hard because in a very un-idlike move they made the normal difficulty of both way too easy.
This! I've also recently played Quake 4 and it's also got some piss poor level design in a spot or two. Just old timey levels where you're sitting around for like 5 minutes trying to figure out the obtuse way you're supposed to advance.