I'd love to see Vaati again. He was such an interesting villain to me, and deserves more recognition. If he could reappear in the child timeline, what's to say he can't reappear in one of the other timelines? Probably not the adult timeline, since it's flooded, but he could very easily reappear in the Downfall timeline. The Palace of the Four Sword hasn't been so much as mentioned in this timeline, but that doesn't mean it doesn't still exist. After all, it wasn't mentioned in OOT, MM, or TP, but then randomly reappeared in FSA. I think there's plenty of room to bring back Vaati. Maybe we'll get a 3D Four Swords game on that timeline or something (I doubt it, but a guy can dream, right?)
I would also like to see Demise again. Throughout the entire series, he has had ~15 minutes of screentime (could be less, could be more, depending on the player), which is a shame because he was such a cool villain! I actually discussed in
an earlier thread the possibilities of Demise appearing in A Link Between Worlds. I am beginning to have my doubts, put the possibility is still there (though I think the Yuga/Hilda combo sort of disproves this). If he doesn't appear in this game, then I would love to see him in Zelda Wii U. He was a very underdeveloped and rather vague character, so I would love to get more explanation. He could, theoretically, appear in all three timelines, given that each one contain the sacred blade that he is sealed within.