This is a fun thread idea!
I'll choose two. My pick for greatest game of all time is The Legend of Zelda: Breath of the Wild on Switch. I would remove any shrine puzzles based on motion controls, clean up the pop-in, and stabilize the frame rate. Other than that, it's perfect.
My personal favorite is Ocarina of Time on N64. I would overhaul the Gerudo stealth sequence, and streamline some of the backtracking necessary to hit 100%










