Comparison pics: https://www.marky.ca/3d/quake2/compare/content.html
The problem was the 3D version looked/looks just plain BLURRY.
Something about my brain is able to understand when they see a pixelated video game that it's an artifice, and give it a ton of benefit of the doubt.
I can't say it is in any way more realistic, but it feels more IMMERSIVE.
Whereas with the higher resolution one, it's an uncanny valley. Everything is too smooth and Barbara Walters-y.
Again, this is my memory of how I perceived it at the time, this isn't modern rose coloured glasses because obviously technology has improved dramatically.