I don't think he'll be back in TotK: There's only place for one big bad guy, using more is detrimental. By using 2 big baddies you don't get "double" the danger, instead each baddie feels less threatening as they´re now not capable of being a worthy threat on their own. In previous Zelda games there was one bad guy who acted at the service of the big baddie (Grahim-Demise, Agahnim-Ganon, Zant-Ganon), there has never been a relation of them being equal in power. The "henchman" posed a threat for much of the game until the big reveal where the real bad guy was exposed and the stakes went up, usually at the end of the game. However this comes at the expense of making the previous bad guy a smaller threat. Ganon is too good a villain, Nintendo can't do that and put Demise as the real bad guy behind it all as that would demote Ganon into henchman status. And by their sheer nature, they can't be presented as equals either, story-wise it makes no sense as, if I remember Skyward Sword correctly, Ganon is sort of the reincarnation of Demise, in a similar way to how Zelda is Hylia and Link is the reincarnation of the goddess' Hero.
It's like how each of Spiderman's villain is a serious threat capable of putting up a good fight on their own, but when you put them in a team their capabilities get diluted the more members you add to the team. The Sinister Six should be able to kill him in a minute; instead they are rarely more dangerous than anything Norman Osborn or Doctor Octopus can come up with on their own.
