The next game is definitely going to be the 3DS one, just because it will be easier to make than the Wii U game. If we're lucky, we might even get a preview of the 3DS game at E3. I for one would prefer the 3DS game to be an interquel set between Phantom Hourglass and Spirit Tracks that officially concludes the Hero of Winds' story, but they've said that it won't be related to previous games in the series, so I'm curious how that will turn out. Hopefully it includes Bellum or Malladus, although Malladus is more likely because asking for another game with Bellum is like asking for another game with Majora or Nightmare. I would actually prefer if it took place after Spirit Tracks and featured Vaati.
The Wii U game will probably be about a whole new Link rather than being a sequel to existing games, just like the 3DS. However, I think it should take place after The Adventure of Link, because the Downfall timeline needs to move forward, and I'd like to see a game that explicitly mentions Ganon's victory in Ocarina of Time.