i think that what it really comes down to is what the question is asking exactly. there are in my opinion 2 ways to ask this question:
which game is better?? and...
which zelda game is better??
do you see the difference?
now when i'm asked a question like this than my answer would be OoT over MM hands down. thats because i view the question as: which makes the better Zelda? of course it would have to be OoT.
OoT is so so much more core to the series. like many have said before me it is traditional. the fact that Link, Ganon, and Zelda herself play such a huge role in this game makes it more true to what a Zelda game is supposed to be. Being the first 3D Zelda, it only makes sense for it to have the type of traditional story that it has. other characters in the game aren't as "intuitive" or "involved" because the game was about character developement with Link, Zelda, and Ganon.
MM on the other hand was also a great game. probably even a better game than OoT...but, its not a core Zelda game. Zelda doesn't even really have anything to do with the story of the game. the world of MM is implied to be some other dimension with a world that seemed doomed to be destroyed. yes this game is very different and very unique as far as story, look, gameplay, and overall feel. thing is that MM does a really good job at improving a game with all of these aspects which makes it a great game. But if this game was not Zeda at all, if Link wasn't the main character, it wouldn't change anything about it. it would still be good, it would still be fun. not that there is anything wrong with that but the fact that it could pass as a non-Zelda makes me choose OoT over MM.
but i'm not saying that thats what it came down to when i made my decision. its just a big factor and i really don't think that many people take this into account when they make this decision. they just choose which one they like more.