I don't think Q2 had nearly as many issues with color as a whole through the game. I mean, it wasn't the most colourful game either on any given screenshot, but it had more biomes and locations. At the very least they learned how to make outdoors look like outdoors, with the bright red skies contrasting with the grey interiors. Later on they even throw a bunch of green lights around when they're feeling frisky.

You're not wrong that Id only stopped making brown games in Quake 3, which if anything is a bit too garish sometimes. I also don't disagree about your description of early shooters, all I'm saying is that people had been getting good at using that cardboard cutout tech and people had gotten good at parsing it. Moving to full 3D required a few steps backwards to then push the tech back past that point, and Quake 1 was a big muddy mess of a game. If you were able to read brutalist eldrich temples as opposed to sand-colored legos that's fair, but even with all the flashy new tech it never read like that to me at the time.