I think a lot of PS1/N64 generation titles - no matter how great - would frankly benefit from some mechanical updates, and *definitely* most SNES-era stuff (as much as I love it!). Even most modern-day stuff. Mechanically perfect games come along only a couple of times a generation.
Vagrant Story, for example, could really use some simple equipment system tutorial stuff and a quick weapon switch. Final Fantasy VI could use some serious rebalancing (and if it got an overhaul, I'd want much more and better character-specific dialogue in the entire second half of the game, where most of the lines being uttered are written for 'generic character.') Devil May Cry 3 could really use style switching.
I'll say: Super Metroid, Silent Hill 2, Resident Evil 4. Most other games I'd want at least some gameplay tweaks, but SM and RE4 both play precisely how they ought to, and for SH2 the gameplay is fairly immaterial to what makes it a masterpiece.