The N64 version is better overall.
The PC version is fun because there are obscure editors out there to let you edit the skins on the characters, and you can patch the game and add MKG character models which makes it a bit nicer.
Also the patch lets it run at higher resolutions than the game could originally, but that's pretty much just magnifying how bad the graphics are.
Also, the PC version, like the PSX version, has FMV endings which is entertaining (ly bad).
But, even with all the patches and updates and new models, the game doesn't really look as good as the N64 version. Even at high res with high-poly count models, it's going to look bad. Damn those miniscule textures.