Not saying that I'd complain at all if skull kid was playable as a new unique zelda newcomer would definitely be welcome but I think skull kid/ majora would work best as a story mode boss fight, as has been suggested before. The fact that he was missing from the moon AT definitely raises suspicions as to whether he'll appear elsewhere but that doesn't necessarily mean him being playable. For a Zelda themed boss, he's far more iconic than Vaati and Pig Ganon already appears as Ganondorf's FS so it's very unlikely that he'd be the boss. The argument that he is 'too small' to be a boss' seems strikingly similar to the debunked argument that 'Ridley is too big'.
He could have been cut as an AT as his boss battle could play very differently than just having the moon crashing, like so:
His boss battle could feature multiple stage hazards like flaming meteors falling down onto the stage, puppets being summoned and he could use his previous AT attack where he flips the view of the stage or even flips the players controls. There'd very likely be a timer for the fight (which would help build a sense of tension similar to MM) and as the battle progresses, the frequency of flaming meteors falling could increase until finally the moon crashes similar to the moon AT but slowed down. His small size could be part of the challenge of the boss fight where you have to try and hit him while he floats around the stage and wails, summoning stage hazards. After enough hits, the second part of the boss fight could have you fighting Majora itself which could play out similar to the final boss battle in MM which I think would be epic.
Would also be amazing if this could happen on a clock-tower stage but I don't know if they'd go through the effort of making a whole clock-tower stage for a boss fight but you never know. Personally, I think this boss fight option would be more true to the character in Majora's mask whilst allowing you to fight both skull kid and Majora separately.
