Majora's Mask is in some ways better than Ocarina of Time, but Ocarina
is a better game overall.
Here's some of things MM is better in:
More things to do (better replay value)
Much, much longer (sorry, but OoT is a pretty short game. Storywise at least.)
The ability to replay story quests, dungeons, and bosses anytime you want (something
that should of been in OoT.)
The ability to play as different species
More instruments
The characters in the story have more personality, including Link (who I swear has almost no emotions in OoT. Especially when he's older. I think older Link was perfected in Twilight Princess btw)
The graphics are better and smoother
The shops are actually useful. (Ocarina's shops are utterly useless. You only need a shop once, and that's it.)
The bosses are actually difficult (cause, let's face it, the bosses in Ocarina are PUSSIES. Although, they are cooler.)
Now here's some of the ways Ocarina is better:
More involving story line
Music is way better (the final battle theme is a.w.e.s.o.m.e.)
Dungeons are better
MORE dungeons and bosses
Hyrule is just better than Termina. SORRY
The bosses are more epic
The graphics are also more epic
The controls are near-perfect
You can save whenever you want (which isn't in MM. BTW, Majora's Mask needs to be arrested for FREEZING ON ME.)
Ocarina can actually be scary
Also, did I mention how AWESOME the final battle is? Did I?
Yeah, the final boss battle is way more awesome in Ocarina (Majora's Wrath is a pretty fun boss too. He's MM's Zant, so to speak. Except Zant provides a better, more cool fight.)
So, that's my opinion.