I liked Majora's mask. I link it in my head to Metroid Prime 2: Echoes or maybe, even, to Mario 2 and Mario Sunshine. With every hardware revolution, it seems that the game makers wanted to make the same game again, but better.
I loved Metroid Prime, but it was essentially a remake of Super Metroid, which was a remake of Metroid. I really like Metroid, so I didn't mind so much... but Prime 2: Echoes was the first (perhaps exlcuding GBA) time that two Metroid games were released for the same platform and I felt like I was finally playing a sequel to Metroid instead of a reboot.
The Mario games haven't fared so well. Mario 2 went a little astray and I don't know of anybody who really likes Sunshine... but I think they came from that same paradigm. Mario64 reinvented original Mario but in 3D and then they went somewhere really new for "the sequel" on Game Cube.
I never played much of the original Legend of Zelda (never had my own NES, and the time I spent on my cousins was mostly spent playing Metorid) and I gave the SNES version a go for an hour or two. Ocarina of Time was the first Zelda game I played very much, let alone completed. Even though I hadn't played the earlier Zelda games, I still saw OoT as essentially a remake of the Zelda story. Majora's Mask felt really different to me in the sense that it was finally a new story and not just a retread.
Sometimes that new direction works and sometimes it doesn't... but I'm always glad that they tried.