I love Majora's Mask on 3DS (still need to find 7 heart pieces and the biggest bomb bag).
They improved lots of stuff. The controls for all three transformations were altered and feel a lot better now. The reshuffling of some item locations is very welcome (makes it easier to collect those Zora eggs before the third dungeon) and the atmosphere on the third day with the red glowing sky is awesome.
I also love how dense the game feels: There is always something to do and it often feels meaningful. The game is packed with stuff to do and doesn't put in any fillers - Wind Waker, by comparison, was full of fillers (not only did it have lots of sailing, it even let you sail to what was supposed to be the third dungeon - and just gave you that stupid orb).
The dungeons are great. The first dungeon is very basic but the others are really good. I enjoyed Great Bay Temple, too! Finding all 15 fairies in each dungeon makes things that much more interesting. And I thoroughly enjoyed the redesigned bosses. Majora's Mask 3D feels more like a new game than a remake at some points.
I wish there was a higher difficulty setting, though. Sure the game is hard at first with only 3 hearts but it gets easy if you finish some side quests. There's, what, 7 bottles in the game? You can get a health upgrade that seals your hearts for half damage after 70% of the main quest. And the Great Fairy Sword can kill some of the mini bosses in two hits :P I refused to wear the secret mask for the final boss battle because that makes the fight way too easy - like a walk in the park (you just spam the B-button...).
I want Grezzo and Nintendo to develop a new OoT / MM like Zelda game based on their current engine. Maybe I'm blinded by nostalgia but I don't enjoy modern Zelda games as much. Majora in particular has a heavy focus on fighting and there were lots of mini bosses in OoT as well. Wind Waker just didn't feel as dense and dangerous. Twilight Princess was a lot better in my opinion but I consider Skyward Sword to be the weakest 3D Zelda game. I feel that with each iteration the series becomes less about growth and overcoming obstacles and feels more and more like a puzzle game that throws "game mechanics" at you just because.