
I don't mean the visual aesthetic part. We all know about fullbrights and overbrights, and has already covered those. It could even be argued that they're a matter of personal preference. Let's get a bit more under the bonnet here.
We shouldn't assume that "because Carmack did it, it must be Good and Right". It was his first commercial and publicly released OpenGL app after all, and he was still learning at the time.
I'll start. R_DrawSequentialPoly - it's evil. A bunch of state changes, texture changes and enabling/disabling TMUs for every surface that is drawn. Far better to make a multitextured equivalent of DrawTextureChains, or even to disable multitexturing.