Well, its just that people HAVENT played MM, and I think its one of the most underappreciated games of the N64. And it seems, judging from SSBM, and several Nintendo interviews, MM does have alot of respect from Miyamoto and Nintendo, I beleive the OOT/Master Quest thing was to make up for the fact that they cant do a Gold cartridge deal (which they SHOULD have done with the Game Boy Color/Advance games)
It can be a standalone port in the bonus disk. Graphics can be updated a little. And like they did with Link's Awakening, the Oracle games, and Link to the Past Advance, they should have a special "Extra" dungeon for beating the game.