Most PSVR games, they all look pretty bad (a few exceptions), yet plenty have amazing game play.

Puzzle games come to mind. I think I spend more time on the arcade cabinet in Catherine than on the actual game.

Fire Emblem Three Houses

No.  Like 98% of indie games are crap in every way.  

But, I get your point.  There are 2% of them that are fun, but only .0001% that have good graphics.  

Judging by the time of release I guess?

Fire Emblem Three Houses.
TLOZ Wind Waker.
Star Fox 64, the terrible graphics were always part of its charm tho.

You don't need AAA graphics to have "good" graphics but the upcoming Bravely Default 2 looks hideous to me. The original BD had very charming visuals on 3DS but what I've seen on the BD2 trailers looks very disappointing, particularly in battle where everything looks plastic.

Several demanding PS4/Xbone ports to Switch end up looking quite muddy, but with the core greatness of the gameplay shining though regardless, such as Witcher 3, Doom 2016, Outer Worlds, and Wolfenstein II.

Skyward Sword, No More Heroes 1 & 2, and Call of Duty Modern Warfare/Black Ops/World at War/MW3 on Wii.

Middle Earth: Shadow of Mordor on Xbox 360.

At the end of the day, I enjoyed all of them, as gameplay matters far more to me than graphics.

Many many many TurboGrafX/PC Engine games. Not that the system could not produce good looking games but it was an 8 bit system at it's core trying to be a 16 bit system so 9/10 Genesis and SNES outclassed it. I think Ys III being a rare exception. It looked and sounded better than the SNES and Genesis versions. In fact the SNES version was the worst of the three funny enough.

It's not a hardware problem. This is just a classic Unreal Engine issue. It's been happening since UE3 and UE4 is no different. Unreal engine has a knack for not loading in textures at times or loading them late. FF7R does not look like that all the time. Just when UE4 decides to wonk out.

mortal shell on ps4 is trash graphics,

Tetris