I don't hate it. Actually, it's in my top five. But I definitely think it's overrated. Having played it well over thirty times, there are several problems that come to light.
The save system is unforgivable. Because of freezing, this game has bad memories for me. Normally, this could be solved by a decent save system. But Majora's Mask lacks this. The Owl Save System completely defeats the purpose of a save system. If my game freezes or the power goes off, the owl doesn't save. It just goes back to the last time you played the song of time. And that's what makes this save system unforgivable. The only real way you can save is by playing the song of time...which means you have to start over.
Not enough focus on the main quest. I'm not that into sidequests. And while Majora's Mask had some good ones, at least half of them could have been scrapped for more dungeons.
It didn't feel like there was a real story. The whole game felt like a bunch of sidequests with no main story and I couldn't stand it. The main story stops the moment you get to the swamp and doesn't resume until you finish the canyon.
I loathed the bosses with the exception of Goht. They were too easy. They had no defense. They felt like overblown minibosses and nothing else...actually, some of the minibosses felt more like bosses than them.
I find myself realizing that Anju and Kafei aren't really the developed and deep characters I thought they were as a kid. In fact, the only real developed characters I could see were Tatl, the Bomb Shop owner, the Swordsman, and the Postman.
Not a bad game by any means. Again, it's one of my favorites, but I definitely think it's overrated.