MM was definitely one of the better Zeldas, and definitely one of my favorites.
The game was so deep; every character a new, eccentric personality for you to get to know over time. You get more connected to the game because it is no longer centered around saving the world, but about preserving the lives of the people you know and love.
Skull Kid/the mask made a great villain. From the very beginning, Skull Kid is putting you down and taking your stuff. But as the game progresses, you learn that he is not just a shallow villain, but a very real, misunderstood character. And the mask that possesses him turns out to be so sinister, it's chilling.
I know the 3-day thing bothered a lot of people, but it turned out to be an interesting element in the game. It put things in perspective, seeing people's everyday lives progress as well as putting you under pressure to save Termina.
Overall, Majora's Mask is one of my favorite Zelda games. And that is why. :]