While I certainly played several shooters (DOOM, Quake, CS) a bit, but not with any passion.

But my favorite early 3D game was Total Annihilation. Which is not a 3D game. It's a 2D game with a 3D rendering engine. Classic RTS isometric POV, but all of the benefits of a 3D engine (arbitrary model rotations, movement dynamics, rockets flying through the air, shrapnel...oh, the shrapnel).

Similarly with Warcraft III, another RTS done with a 3D engine. Its gift was the interstitial cinematics done with the engine for story telling purposes.

In both these cases, 3D added immensely to an ostensibly 2D experience. I also imagine once they got things sorted out, it made things much easier for the level and scenario designers to be able to just put Objects into their flat-with-some-terrain 3D worlds.