Story: This was a very hard choice for me because they both had great stories, but Majora's Masks great strong points was the story, it seemed the developers focused more on story and depth than OoT. So MM gets the point for story.
Graphics: Majora's Mask made use of the expansion pack which gave more detail to the graphics. MM gets the point.
Gameplay: Ocarina of Time had great gameplay with turning into an adult and all, but in MM you could turn into 3 races with the use of different masks which I think is better than turning into an adult because it gave you more of a variety of options and puzzles to solve. Majora's Mask gets the point again.
Difficulty: Okay this is going to be kind of repetetive, but Majora's MAsk was the more challenging of the two, and I like challenge in the games I play, MM again.
Nostalgia: Honestly, I have more memories of playing Ocarina of Time when I was younger, and I don't have many nostalgiac memories of playing MM, so finally a point for OoT.
Conclusion: All and all, MM was the better of the two games, I don't hate OoT, I just have come to appreciate MM more over time that's all.
-Tony