Probably Doom, as it was one of the first FPS games and it did a lot of things right.
Oh, and as a response to the whole Halo worshipping:
1) Don't you ever dare to say that the vehicles were good. They sucked beyond comprehension. The controls were plain bad and they were pretty damned useless most of the time. Why the hell would space marines be using 4x4 cars with absolutely no friction? The tires on these things are massive, yet it always seemed as if you were driving on ice.
2) Good AI? The AI was an abomination. Enemies acted retardedly and allied units were just as stupid. I remember that at one point there was a mission where the played would have many, many allied marines on his side, and they would all die thanks to their stupidity, id est by running straight into the enemy.
3) Weapon limit, oh my! This would indeed be something nice, were it not for the fact that you could find every damned weapon in nearly every room. I would often run out of ammo, and replacing a weapon would be no problem whatsoever, because there were piles of weapons all over the place. So much for your awesome weapon limit.
4) Grenades were quite nice, but not always useful. I often prefered to just barge into a room with a shotgun than to throw several grenades. The grenades were by no means better than the ones in Medal of Honor for the PS...
5) Weapon balance sucked. There were 3 weapons I used while playing the game, because the others were simply worse and therefore there was no point in using these other weapons.
6) I found the soundtrack very unfitting. At some points I thought it was Enya or whatever. Does Enya fit the mood when you're at war with aliens? I don't think so!
7) Here's some more innovation: The same rooms are re-used dozens of times. I lost count of how many times I had to run across a bridge that looked exactly the same as several bridges I had seen before. The same goes for many other rooms. This made the game look rather repetitive.
8) The health system ruined the game. You could screw up and hide for a second and everything would be okay. This made it far too easy to get past certain points.