Doom used 2D sprites, so "fake 3d" if you ask me.
Quake was a whole new paradigm, it was based on a true 3D engine and its maps were generated in three dimensions. You could stand under stairs, under the room above, and underneath lifts.
Grass and particle effects are secondary....
How many FPS AAA titles today use sprites for enemies and weapons?
Nothing's stopping someone from adding code to render 3D models or "portals" in the game, and in fact it has already been done, with no 3D acceleration needed.