The only era I have a problem with is 5th gen . The PS1 is the greatest offender. While most N64 games accepted the idea of low textures on large polygons and use of a bright, limited color palette, the PS1 tried too hard to make realistic looking 3D stuff long before the tech was there. Being as this is EoFF I'll cite FFVIII. It was so much worse than VII or IX just because it tried to hard to make realistic characters. It was far from the only one though.

I understand why gaming made the push to 3D before it was technically ready, but I still rue the decision. The SNES looks fantastic and the graphics have aged very well. Even a lot of NES games have aged very well in comparison to PS1 titles.

I've been trying to catch up on the MGS franchise, but FML when I try to play MGS1. It looks and controls terribly.

That's another issue of that generation (once again worse on the PS1). This is before people had figured out how to optimize twin-stick control of 3D worlds. A lot of games ended up with tank controls or worse.