Going off of how some Assists people want upgraded, such as Isaac or Bomberman, are player characters in the games they appear in, I just had a thought:
What if there was a game where Skull Kid was the player character?
(Fair warning: I'm a fan of philosophy/psychology so this idea heavily leans on that.)
I could see a game focused around Skull Kid would be similar in layout to The Legend of Zelda, Majora's Mask (3D, open world, etc.), but it would reply heavily on the psychological aspect. You start off as Skull Kid stealing the mask from the Happy Mask Salesman, and then travel to Termina. Regarding the question of whether Termina is real or it was an illusion created by Majora (as that non-canon encyclopedia seems to imply), the game would borrow aspects of both. Termina would be shown to be an actual place, a parallel to Hyrule as implied in the game itself, but it becomes a bit more distorted and strange as we see it from the perspective of Skull Kid's psyche. We get a sense of how Termina actually is versus how Skull Kid sees it to be with Majora's "help". The Field of the Moon Children, or at least an area similar to that, could act like a sort of hub world, or an area where Majora and Skull Kid talk. You'd get stronger from Majora essentially granting Skull Kid new abilities as part of their game, preying on his loneliness and putting up a front as his friend, though really being more of an enchantress putting him under a spell.
While the game would have "dungeons", so to speak, all of them gone through are all manifestations of Skull Kid's psyche that he has to confront. His former friendship with the giants (and Tael who he'd be separated from that that point), his sorrows, his liking for playing pranks that increases and becomes warped as Majora's power takes over him. As the days progress and the Moon draws closer, Majora's power over Skull Kid's mind becomes more overt. The final battle could be like a "Battle in the Center of the Mind", which culminates in Skull Kid having to fight a merged manifestation of himself and Majora as the Moon descends upon Termina. Following Majora's defeat (Skull-jora? I don't know), the game would end in a similar fashion to Majora's Mask.
Think the original
Majora's Mask mixed with
American McGee's Alice, and you basically have what I think would be a cool game centered around our favorite forest imp.
Heck, even though this will likely never happen I even did a logo/cover art with a tagline because why not.
Image isn't showing up for some reason on here so have a link instead.
(I would have called it "Terrible Fate" but there's that excellent Skull Kid short film by that name already.) I wrestled with about 3 different tagline options before I picked this one. Honestly if this kind of thing was done as a fan project (even just like with Source Film Maker since I know people have made Zelda assets for that) I'd totally watch/play it.
EDIT: What the heck, I compose music so maybe I'll do a concept album in the future based around how it would go.