The better question is which MGS2 and MGS3, the original or subsistance versions. It's be a shame to put these out and not go all out on the available bonus features (if not add some new ones, but I won't hold my breath.) At least make sure all games have a theatre mode.
And, yeah, MGS1 will need either a complete rework, or the GC version with a lot of tinkering to remove a few things. Kojima will probably insist on updating the nuclear stats, and we'll need new things for Mantis to torment us with (not to mention the controler port thing).