Majora's Mask is easily my favorite Zelda game. I didn't even play it properly until a few years back, but it still managed to overcome the "nostalgia factor" of all the other Zelda games I'd played. And I'm a pretty dang nostalgic guy, too; it's rare that my old favorites ever get dethroned, but that's what Majora's Mask did.
I never played it much as a kid because I couldn't understand the game mechanics. And it scared me. My memories of playing it as a kid are just a surreal blur of clock town and the moon. I'm thankful I gave it another chance once I got back into the series, because it skyrocketed to my number #1 spot in the franchise after I spent more time playing it.
When I started playing again the time limit did seem really annoying. Then I realized there were ways to work around the limit that helped ease me into the process, and I became intrigued by the nuances of the NPCs. How they would react differently based on what day it was and what they were doing. Impressive for an N64 game, I thought.
I think it was after I first beat woodfall temple that the design of the game really hit me with a sense of awe. Termina, as a world, is pretty small, but very memorable. Hyrule field is great but it's not as unique as the oddly structured world in Majora's Mask. There are great dungeons in every Zelda, but the ones in Majora are by far my favorite. Design-wise they were all very unique and while they still followed some of the old Zelda-dungeon guidelines (forest, water, etc), they were all handled exceptionally well and stand out as, imo, the most unique and memorable of any Zelda game. Inverted stone tower temple, anyone?
The difficulty is almost a perfect balance, although near the end of the game it did feel a bit tedious at times with some of the quests involving Ikana and climbing the stone tower. However, it all added to the overall experience, and the majority of the game isn't unfairly hard, though it's also never mercifully easy.
And of course, the atmosphere. I could go on and on about the atmosphere. There's something about Majora's Mask that I can only describe as primal, in a way. Does anyone else feel that? There's a primal nature to a lot of the design, meshed with somewhat familiar, albeit stylized, themes from OoT. I don't know if that makes sense to anyone else but me, but yeah. The game has a very dark, but not depressing, tone. It's stylish but not annoyingly so; it's subtle in ways, but there are moments when the artistic quality of the game really hit home for me.
Whenever I compare it to any other Zelda game it stands out. I love the series, but Majora is especially notable for me because it breaks from the pack so proudly. Eiji wasn't afraid to create something entirely different after OoT, and I respect that, because he could have easily just created more of the same and cashed in on that. Instead, he created something entirely unique with gameplay mechanics that not everyone would be comfortable with. He took a shorter development period and turned it to his advantage, creating a mesmerizing Zelda experience that doesn't seem cheap. Even though it recycles character models, it works exceptionally well and adds more of a surreal twinge to the game.
It's filled with more expression than 99% of games I've played, and it conveys it all through atmosphere and design. It was technologically almost outdated the moment it arrived, as the N64 was on its way out, but it's one of those games that just can't be defined by aging. It's so unique that the game design will always seem different, with an explanation for every "limitation" that you grow to embrace.
I could go on and on, but I'll end it there.