When we look at them now especially on HD tvs the SNES games look better and cleaner. At the time, Mario 64 and Resident Evil 1 absolutely blew me away.

Because unlocking the 3rd dimension was magic that changed gaming forever. CGI cutscenes and voice acting also got gaming closer to movies, which was unimaginable.

Games with prerendered backgrounds still look good to me. Chrono Cross is stunning, an audiovisual masterpiece.

Agreed. The pixel graphics of the 16-bit era have aged very well. I dare say they are timeless. I can still look at games like Super Mario World, Sonic the Hedgehog 2, Super Metroid, A Link to the Past, and Chrono Trigger and still go "This looks really nice."

Meanwhile, even at the time I was not terribly impressed by early 3D graphics, and time has done them no favors. They textures were awful and the low poly count models looked rough. I felt this was even worse in general on the PS1, though the N64 had its own problem with excessive fog in many games to cover up the low draw distance. The games that fared best visually were the ones that went for a deliberately cartoon-y aesthetic with flat textures, like Super Mario 64 or most of FF7 (the overworld looked terrible). Also, I will give the PS1 credit for supporting pre-rendered backgrounds, which often looked much nicer than the actual 3D models, plus the system did still have a few games with 2D pixel-based graphics, like Mega Man 8 and Symphony of the Night.

Honestly, I felt the industry abandoned 2D pixel graphics way too quickly. I guess they had to start somewhere, and making games in 3D was a learning process with a lot of stumbling blocks both in terms of visuals and gameplay. Still, the few companies that kept making 2D games showed it was still viable and there was still progress to be made even on that front. For example, Street Fighter III to this day still has some of the finest pixel art and sprite work of any game ever, and I still think it looks better than more modern SF games.

That's a silly take. 2D PS1 games generally look much better than 2D SNES games. You should compare like with like. Are you going to say Star Fox looks better than 3D PS1 games?

Yeah you sorta see something similar with a lot of new technologies, like how really good baked lighting can look better than not-so-great realtime lighting.

A game like Metroid Prime Remastered looks incredible while running at 60fps on the outdated Switch 1 simply cos of really good artist-driven baked lighting, and avoids a lot of the pitfalls that realtime GI can cause.

For 2D games maybe, but try playing like Star Fox or Stunt Race FX on the Super NES and tell me Star Fox 64 and Wave Race 64 aren't light years better.

Even 2D games, like Killer Instinct Gold looks miles better than Killer Instinct (SNES). I do kinda wish we got a 2D Donkey Kong Country on the N64. 

Very true.

2D games perhaps look better due to the low poly games of the fifth generation, obviously not 3D SNES games (the few there were). And PS1 and Saturn had better looking 2D games than SNES.

Started up tales of phantasia on the snes and WOOW.
Dayum this game looks gorgous

The original Donkey Kong Country trilogy still looks good.