I enjoyed Majora's Mask a little more than OoT...
First of all, I thought the characters felt more alive than in any other Zelda. They all had their own problems and they were sidequests. You had some sort of bound with the characters, which I really appreaciated.
The 3 days cycle wasn't that bad once you know the right Ocarina songs. It also added also some state of emergency unlike the other Zelda, were you can take all the time you need.
The tranformation masks were quite fun, I really liked being a Zora! (They're my fav race.) Most of the masks were useful, beside the couple's mask which I really was dissapointed in. The mask wasn't worth all the work.
The graphics and the effects were really pretty, I liked the room were you meet the Giants and the inside of the Moon. They had a surreal feel... Also the game had an overall dark/sad atmosfere which I really liked.
Finally, that's why I prefer MM over the other Zelda, even though I enjoy them all!
