For me, it's the darkness in the game. There's a palpable sense of doom and sadness; the atmosphere is simply mystifying. I also like how everything you do has consequences, as you can see using the Bomber's Notebook. If you do one thing, it opens up some sidequests and closes down others. In that way, it's more realistic than
OoT, because people act differently depending on the day, and you can influence them depending on what you do.
It's hard to exactly say why I prefer
MM to
OoT, but the atmosphere of the game has a lot to do with it. And I think that's why so many people like it: it's a Zelda game with a darker story and more maturity. And the three-day system is so unique and intriguing; it's one of those games with an experience you can't get anywhere else.