Calamity Gannon makes more sense to fit this type of role as a boss imo
Especially with Breath of the Wild being the newest and hottest LoZ game.
We've got pretty heavy representation for BotW already. I can see an assist from one of the Champions or Guardians as well.
So far everything just works for Skull Kid.
-Link redesigned to his BotW incarnation/BotW stage + Music to accompany it(Thus giving us BotW rep)
-Midna and the Moon as assists
-Young Link's FS is M.I.A.
-Sakurai clearly knows his popularity, as similar to Waluigi, they've been among the first deconfirms in the past(Skull Kid with Wii U/3DS and Waluigi with Ultimate)
-High demand for a new playable LoZ character
-Majora's Mask released on 3DS around the time we've got an idea of when the roster was potentially finalized
-Comes from one of the most recognizable and iconic games of the series to the point Majora's Mask is as recognizable as the Triforce