I will venture here a heretical opinion: Changing a game like Doom/Doom2 to a true 3D engine is bound to make the gameplay worse. Why is that? In deathmatch, depending upon looking up and down will complicate things too much until a better way of controling the freelook than the mouse is invented and becomes widespread. In real life, 3D space doesn't present any challenge since we all have side vision, but there is no such thing in computer games, where the field of vision is restricted with the monitor frame. The 2D maps of Doom/Doom2 blend in with the limited vision angle perfectly, allowing the player to forget all about the controls and move freely, making the illusion of life even more complete. Adding an extra dimension makes it harder for a player to adjust to a new level, harder to control the game, and so much easier to lose the other player.
Doom2's gameplay superiority over Quake1
In true 3D worlds, camping will rule. If a camper takes a drop on you from somewhere above you, no amount of skill will allow you to retaliate with the necessary speed and precision. It is NOT what imitates real life that people are looking for in these games. What they are looking for is an alternative that is just as interesting to explore, an alternative that forces a player to develop new abilities that are just as hard to perfect as any real-life skill. The movement bugs in Doom -- the strafe-run and the wall-run -- have given it such a sweet personality. Are they anywhere near real life? No, they are not. But take them away, and Doom will instantly lose a huge chunk of its charm.
Deathmatch is a form of martial arts, and is ruled by the martial arts philosophy. After the newbie's exhilaration from the fact that he can truly interact with that bfg-wielding avatar on his screen wears off, the long and tedious road of developing true deathmatch skills begins. Perfecting one's movement and aiming techniques is step one of the many steps on the ladder. Acquiring good strategy and learning to play advanced psychological game lies further ahead. The player in Doom2 is fragile. He can be taken out with one shot. As the average doomer's aiming skills improve, playing a defensive game becomes a must, opening up a whole new world of strategic traps and evasive manuevers.
NONE of that has been passed along to Quake, the bastard son of the same great gods who created Doom. The player in Quake takes too many shots to bring him down. Therefore, he is not afraid of the other player, and there is no need to dodge. The only weapon that can kill you in one shot, the all-powerful rocket launcher, is all but impossible to dodge (another unwanted side-effect of true 3D). To make things worse, they could only make the rockets transparent. Quake is the bad twin brother of Doom, that collected all genetic garbage that was left over. Triangles SUCK for making sprites. I could embrace the idea of a true 3D model for a missile, but for the player? Get real. He doesn't look like a human being anymore. Even the blocky chump's cry of death and waving hands do not convince me: he has got bricks sticking out of his body everywhere; he is not real. And the slight bouncing of weapons in Doom, that makes you feel like you are really running, where has it gone in Quake? Why does a weapon move back and forth in this sickening fashion in front of me? It makes me feel like a mental patient masturbating with his bazooka...
...Quake was released as a deathmatch experiment. I say, the experiment proved that all its new takes at deathmatch were wrong. Doom2 is still the game for the time being, and, unless a new game granting my above wishes for perfection will be released, is going to remain the deathmatch game of choice for a long time. Quake is, and will remain, the first game in history implemented with open architecture, allowing players to modify it the way they see fit. It is not the great idea behind this customizability that I am bashing. It is the particular implementation by particular people. Should someone create a Quake clone that looks and feels like the Doom, I will be among the first to start playing it.