Majora's Mask is great because of its atmosphere, and how weird and personal it is. The game isn't really about the dungeons (which are pretty nice, and definitely follow the "weirdness" theme of the rest of the game, even though they were harder than
Ocarina's), it's about the people. Most NPCs in the game actually has some role to fill, unlike in other
Zelda games where they mostly just have space to fill. The gameplay is pretty much the same as in
Ocarina, plus the transformation masks, which are basically the same as the time-travelling in
Ocarina (it gives you some new/different abilities and affects which items you can use; plus the "cosmetic" change), but you can do it anytime, and there are four different modes (five, if you count the Fierce Deity). The "short" time frame (with the Inverted Song of Time, you have like two and a half hours to fool around before you have to go back) is also for the sake of the people in the world. It would have been impossible to keep them interesting if the time would have kept going indefinitely, so it has to be rewound. I was never bothered by it, and it made for a very nice ending, where finally, a new day can dawn (yay).
There are also lots of emotional moments in there. Easily more and better than in any other
Zelda game (maybe
Link's Awakening comes close, with that rather sad ending and all). For instance, every transformation mask you get, you get by "healing someone's sorrows", which actually means
letting them die. Or that mutated mummy that comes out of a closet making
horrible noises, that turns out to be the little girl's father.
In fact, there are lots of ghosts, and dead people, and ninja ghosts, and aliens, and I think it's great. So I was a bit disappointed with
Twilight Princess, when it turned out that the "ghosts" were actually just people that weren't dead at all (they were in the second trailer, and I'm pretty sure that they were supposed to be ghosts at that point, because they looked
dead; and what happened to that spider chase, dogdamnit?), and everything would be fine again (everything isn't fine again when
Majora's Mask ends; dead people stay dead), and nothing would have any consequences. The Yeti part, and when Ilia gets her memory back was nice though, but in
Majora's Mask those things would have been side quests, not plot critical (especially Ilia's memory), and you would have been able to do them again and again, without having to play through the whole game (another thing I which think is neat).
On the subject of controls, I'll just note that I liked the precision of the N64 controller. Aiming was easy with that, but when you try to turn just a little bit with the Gamecube controller, it either turns nothing at all, or way too much. It also was the coolest looking thing ever. Too bad it broke down so easily.