If they did remake it, I'd like for there to be a better explanation for why everyone splits up. Like, what do they do if they aren't with Cloud?
Secret of Mana is definitely up there, too. So much cut content. So much.
Sometimes games just need small tweaks, though. Like how in the DS version of Resident Evil 1, they map the knife to a shoulder button instead of making the player switch to it through the menu whenever they want to use it. Or how in the Dreamcast versions of all the RE games from 1 to 3, you can check your health and ammo.