Hi, I'm new here, but I'd like to give my $.02 on the debate. I think people are confusing a good game with an important game. There is a difference. Some games like Super Mario 64 are more important games than good games. Super Mario 64 set the standard for platformer games and used an ingenious camera system. Another game that's more important than good is Doom. Doom really set standard for first person shooters in general. I think many of the great games of all time are great more because of their role in video gaming as a whole rather than the game being just good.
An example of a just plain good game is GTA IV. GTA had been around for a while as did the whole sandbox genre, but GTA IV was just a freaking amazing game. There wasn't much originality in GTA IV but Rockstar took the original formula and fed it steroids. Another example is Super Mario Galaxy and Super Mario Galaxy 2. I think Super Mario Galaxy is more important than it is good yet Super Mario Galaxy 2 was just plain good. In fact, some reviews don't give Super Mario Galaxy 2 perfect scores because it didn't have the originality and significance the original Super Mario Galaxy had. And I feel Mario Galaxy's score was inflated due to the sheer originality of the whole "Mario in space" concept. My point is that sometimes games get such high ratings because they did something important and significant rather than something well. And many a time a game of the same genre with a similar plot and gameplay comes out a year later on the same console and gets a lower score even though it had better gameplay, graphics, music etc. because it didn't have the impact the original game had.
I think OoT is a more important game than a good game. Zelda OoT took the Zelda series and made one heck of a leap into a huge, beautiful 3D world with amazing controls, music, and gameplay. The Z targeting system was ingenious, the vast world with tons of dungeons was unheard of (at least for the N64), and the harmony of everything that makes an adventure game; gameplay, music, graphics, controls, storyline, sidequests, etc. was fantastically exquisite and nearly perfect. Though MM's 3 day time system was original, it was too specific to MM for it to be revolutionary for video games as a whole and was too hit-or-miss in regards to gamers liking the concept to have the impact the universally acclaimed Zelda OoT had.
Though I feel OoT is fantastic and one of the greatest games of all time, I think people confuse its being important as it being good. I personally feel MM is the superior game. It was emotional, beautiful, fun, challenging, gloomy (I mean that as a quality), and has a heart and soul of its own. Though MM had fewer dungeons, getting to the dungeons is as puzzling, frustrating, and lengthy as the dungeons themselves. MM sucked you into the story rather than having you follow it. MM to me is a love-hate game. You either love it or hate it. Some people hate the 3 day time system and the frustration it brings yet some people are entranced by it and in love with it. Some people hate the fact there are fewer dungeons yet some people love the tough challenge it is to get there as well as the far more challenging dungeons than what OoT had to offer. And some people just prefer linear games over ones you have to kind of figure out on your own. OoT is far more linear than MM and some people prefer being told where to go (for the most part) rather than having to piece things out themselves.
Don't get me wrong, I think both games are fantastic and belong in the handful of games considered the best of all time, but I give a slight edge to MM, mainly because of its story. It's not as much that the dungeons were huge, challenging, and lengthy. It's not as much the improved graphics, new songs, and vast new overworlds that are Termina and Clocktown. And it's not even the fact it's so original with its 3 day time system. I think MM's story is outright touching and tear-jerking while at the same time being dark and thrilling. OoT is the generic "Evil villain takes over X and you're the last hope to you to stop him/her." MM is the story of how sadness, loneliness, love, courage, loyalty and friendship can conquer the very soul of a character. MM isn't about good vs. evil, it's about the importance of love and friendship in all of our lives. MM executes that perfectly and turns a simple video game into a heart-throbbing, exhilarating adventure that can take over you for days at a time. It's very rare to find games with such deep, personable stories and that alone is why MM is the superior game to OoT. Oh, and Skullkid is the invaluable friend MM is referring to for those who don't know or aren't sure.
And again, I think many of you are confusing important games with good games. Many of the responses have said "OoT is better because it's the first 3D Zelda" or something along those lines, but that isn't the question. The question is which game is better. Or had this been about which is a better Zelda game then OoT would definitely be the answer. But this is about which game is better and I think the components (the 3-day system, the story, the dark and gloomy environment, etc.) all work in perfect harmony to make MM the superior game.
Again, this is just my opinion.