Well, here's how I compare Ocarina of Time and Majora's Mask...
Ocarina of Time was groundbreaking in the time it was released. A 3D Zelda! The game introduced a ton of music that would later become marks of the franchise. Zelda's Lullaby, Song of Storms, and Saria's Song, and the Song of Time being the most notable. The gameplay was good, and compared to MM, the dungeons were far more memorable and superior in design. It was a beautiful game.
HOWEVER. Majora's Mask took OOT's gameplay and only IMPROVED it. And even though it still had good music, such as Clock Town or the Song of Healing, none of the themes became staples to the series. The dungeon design was typically sloppy... at least compared to OOT. 2 out of the 4 dungeons were pretty lackluster... these being Woodfall and Snowhead. The next two, however, were very advanced in design, easily rivaling OOT. But it's still only 2 out of 4... Now here's where MM REALLY shines. The plot. The plot was tragically beautiful, and way better than OOT's generic story. (Not to mention MM's final boss was much less of a disappointment than OOT's) And the characters, unlike those in OOT, really came to life. If any Zelda game should be made into a movie, it's MM.
I think the main reason OOT has so much hype is because it was the first 3D Zelda game. It's groundbreaking! But MM was still a great game, it just didn't have the same feeling of "something new".
If you ask me, Majora's Mask is the better game. You can really connect with those characters around you and with the plot itself. Although, as far as dungeons and overworld segments go... OOT wins. It had better design. And the fact that MM was made in one year is a good excuse for that. So really, what it all comes down to is what the individual player thinks is more important... a compelling story or genius design.