Ganon will return. I'm sure of it.
I have a two ways that I would probably do his return. Both involving a corrupt king.
My first is that the triforce immediately returned to him after making his wish, the fact that it appears in the wind waker on the back of his hand during the final battle was in fact deliberate. The removal of the master sword from his head would mean his return. Of course he is under the great sea how on earth would the sword be removed for him to return? If I were in charge of this story it would go something like: King Daphnes wished for old Hyrule to be washed away, not immersed in water for the rest of time, just washed away. This would mean eventually the waters would recede leaving behind bare land and of course the master sword embedded in Ganondorf will still be there, so a temple to protect this will have been built. Both new and old Hyrule will be colonised. A secondary villain, perhaps a usurper king of Hyrule will want to resurrect Ganon. Perhaps because he is a descendant of a line of Ganon supporters or a really good plot twist would be to actually use Ganon to assemble the triforce so the Usurper king can make a wish.
My second is that although the triforce left him Ganondorf retained his powers from it, this would explain why he did not just die after a single light arrow and how he could take such a beating with the master sword, and still need it firmly embedded into his skull to stop him. his spirit is sealed within his body by the master sword. If I were to do a story for this one the great sea would still be in place. New Hyrule will have been conquered by an evil warlord who has made himself king. He has found and assembled the full triforce. He has heard legends of Old Hyrule and wants to expand his territory by taking that as well. So he would of course wish for old Hyrule to be uncovered. Of course during the exploration of these new lands the master sword will become removed from Ganondorf's head allowing his spirit to escape it's imprisonment. In this Game old hyrule will become Ganon territory, a world full of monsters, and the new Hyrule part will be the more peaceful area link must stop from being consumed by Ganon.
Well those would deal with how to make Ganon return on the AT. I'm positive that if they make more AT games they shall find a way to do so.