If this game is ever remade, then I think it definitely should have a Master Quest. There would be no reason to leave it out of the deal.
The changes the Master Quest brings would probably be akin to those in Ocarina of Time 3D. Stronger enemies, altered dungeons, and a mirrored world. I think the mirrored world would be especially difficult for me, considering how complex the dungeon layouts can be. Stone Tower Temple and its inverted form come to mind first. The stronger enemies would be nice, and the altered dungeons would be refreshing.