Umm, yeah Majora's Mask is better than Ocarina Of Time, my reasons:
Better Art - it's so surreal, colourful, bizzare, OOT was pretty plain in this respect.
Better Music - Subjective too, but come on, Clock Town, remixed Hyrule tune, Song of Healing... lovely.
More challenging - more satisfaction in that respect :p
Better storyline - Yup, the storyline was fully integrated in the gameplay, they work hand in hand, so it worked beautifully and was emotionally charged.
The usage of Time - The three day system is the most innovative Idea ever conceived in my opinion, watching each character's drama unfold depending on whether or not you chip in and help is immensely satisfying and organic too, the characters here have a life, they are not cardboard cut outs like in OOT for the most part.
Much darker and much more atmospheric.
Granted, I loved OOT, but MM just stands out more, OOT felt like alttp in 3D.
Protecting the Ranch was quite scary and surreal in a way, I loved that :p
Also, following Cremia to deliver the Milk was such a treat, MM's side quest are awesome.
Oh and Stone Tower is my favourite dungeon in any Zelda game.
Oh and while the LE version looks much better than the original content, the N64 has better frame rate, no bugs, no sketchy music and a more balanced control system. I got an N64 copy and I wasn't disappointed about it.