Can't current emulators already do graphics replacement? I know I've seen it with N64 emus.
It'd probably be doable. I've seen a project out there that's an engine for running FF7 PS1 discs on PC without emulation. It's on Linux Game Tome somewhere.
Dunno about replacement MD3 models, though. Not only would that be a huge-scale undertaking, but it'd require the game to be changed in so many ways to not look really goofy, and at that point it'd probably be better to just buy FFIV DS
