Honestly Majora's Mask's "story" is mostly judged by the experiences people had with the side-quests. They all relate to the cyclical framework of its narrative but ultimately they don't directly influence the critical path. If you strictly look at the main path it's basically "Kid gets bullied; kid grew apart from friend: Kid reconciles his misdeeds; kid finds a new friend".
It's alright but the execution always leaves me feeling slightly emptier than I feel I should once the game lands on its "The End" screen with that weird Kokiri jingle.
I do actually hold Ocarina of Time above MM in terms of raw storytelling although it's a more generic framework.
Wind Waker is the best one for me closely followed by the N64 games and Link's Awakening. Quite a lot of side-dialogue in Wind Waker reaffirms that Link is being dragged into his "destiny" and on second-playthroughs when you can read the Hylian text, the fish-gods all talk to his boat, the King of Red Lions in a cautious manner. "So, you really want to bring the boy into this?" and such. It all culminates in that fantastic endgame where you see the contrast between the King and Ganon and the game finally reveals that the Zelda mythos and the imposed destinies it brings does more harm than good. In a sense it deconstructs Zelda and ends on a freeing note, that the future for all children belongs to them and not the guardians who grew up in a different time. It's such a universal idea and not something you see as the "main theme" that often in storytelling, at least not in a heroic fantasy. It ends the game on a strong note.
By the Goddess I hope BOTW2 features another complex Ganon
I think when people keep saying this you're understandably thinking of WW Ganondorf but really, in a sense what you're asking for is just another retelling of Wind Waker then. Imagine if Ganondorf appeared 6 times as a complicated villain and each time his motivation is completely different. One time he's a thief who wanted to represent a poor people with might. Another time he's a tragic hero that was denied by gods. Another time he's an old man stuck in an infinite time loop that made him lose all he cared for. etc.
I just don't want Ganondorf to become an "idea-sponge", essentially. I think it's cool if BoTW just goes with the idea that this "Malice" swallowed up Ganondorf's corpse and reanimates it - then the characters of the story suggest the myth behind Ganondorf and his Gerudo roots, but the core of the story revolves around someone else than him. More than anything I would love another Zant but without ruining their agency at the 11th hour through Ganon.