I am going to have to say Chrono Trigger. Everything about the sprite work from appearance to animations is nothing short of spectacular, and the environments were beautifully crafted. Just compare it to other SNES games from the same genre, and that is all the proof that you will need to see that visually, Chrono Trigger was a step ahead of the rest.

Donkey Kong Country 2 looked like a PS1 game

Personally, the game I remember as a kid was Daytona USA in arcades. Was like '94 and was use to simple PC games or SNES.

Splinter Cell

Metroid Prime of course
and
Jak & Daxter - the level streaming technology with that LOD on both foreground and background on a PS2 was insane.

Submarine Titans looks stunning for an RTS of the 2000s.

This is tough. It's hard to determine if a game is ahead of its time or ifa game is just the best looking game of its time.

I'm still gonna say Jet Set Radio. That cell shaded look was unlike anything I'd seen before and would eventually be used in tons of games. Ahead of its time? I don't know. Just innovative, I guess.

Virtua Fighter 2 was mindblowing for its time. The arcade version was outstanding in itself, but the 1995 Sega Saturn version was nuts. Some of the finest, if not the finest character modelling of the entire generation, on top of that the games was rendered in a whopping 704x480 !!! (704x512 for PAL) and of course a solid 60 fps:

And obviously Daytona USA, Arcade version. Unbelievable that this game was released in 1993, it was fully 3D and was released same year as Doom, and a year before Donkey Kong Country, it looks like a Dreamcast game.

Along with SEGA, Namco was also ahead of the time in the 90's. Soul Calibur on the Dreamcast was of course exceptional for a 1999 Dreamcast game:

Stylistically, I think the following were really ahead of their time. They hence hold up really well, despite the limitations of the hardware:

I had to look that one up, as I hadn't heard of it before and wow, it really does look pretty dang good for it's time. I also just found out it released on Steam this yr too, so I might have to pick this little gem up.

https://store.steampowered.com/app/1259380/Submarine_Titans/

Thanks for bringing it up, otherwise I wouldn't have come across this nugget of RTS goodness. 

The Donkey Kong Country games on SNES.