I'm AMAZED (and kind of relieved) that OoT isn't #1. I voted for MM. OoT is actually my least favorite 3D Zelda game. Here's a list of why I love MM more than any video game PERIODD:
1. The bunny hood. Whenever I play any other Zelda game I'm frustrated by walking slowly 'cause I'm so used to MM.
2. Depth/emotion/darkness. I think MM was the darkest Zelda game. This is a plus for me because it brings emotion and depth. It's not fairy-tale-like like OoT or WW. You could actually feel the emotions of the characters and their agony and dispair for the end of the world. There were so many cutscenes like with Anju and Kafei, Pamela and her father, etc. that made the game more interesting. This is probably the main reason I can't finish OoT; I can't play it long enough to finish it because it's just dull to me.
3. Music. The music of MM was better than OoT IMO. Even though OoT had Gerudo Valley, Spirit Temple, etc... MM had an amazing soundtrack that topped oot. (Song of Healing, Oath to Order, Stone Tower Temple, Clock Town, Elegy of Emptiness, Final Hours, etc.) It really set the mood, especially the sad ones.
4. Graphics. Technically they were slightly improved. Stuff further away could be seen, things were more detailed, etc. Not a big deal but still..
5. EPIC. I've heard people loved OoT because of its epic story. But COME ON! What's more epic than the apocalypse?
6. Sidequests. MM had the most sidequests (although WW had a lot too). It makes me feel more in control and free instead of doing everything in a set order. Plus the Anju and Kafei story was pretty amazing.
7. Difficulty. Although it's not really a difficult game, it's definitely more difficult than oot, ww, or tp. Much more of a challenge.
8.Character development. The use of time helped make characters more interesting. For example, you could find the Gorman guy at the stock pot inn in the morning, at the town hall shortly after and at the milk bar by night. Every time you saw him, he was doing and saying different things. Example 2: The postman could be found in many places. Throughout the day he slept, practiced, delivered mail and picked up mail. What he did could also be altered by what you did. In all other zelda games, they just stand in the same place, saying the same things over and over again. MM really felt more realistic. Everything was moving and changing.
9. Complexity. Everything flowed together. All of the different stories around clock town seemed to relate to each other and you could even affect the flow of events.
Why do people love OoT? Because it came first. It was the first leap into the 3D world. It was "revolutionary". But to me, MM surpasses OoT in almost every aspect. It's been 12 years since OoT. I don't play a game and favor it because it was revolutionary over a decade ago. I favor MM because of the reasons listed above. But hey, it's just my opinion. Maybe I just like it more because it was my first one. Idk.