Speaking with Game Informer magazine, The Legend of Zelda series producer, Eiji Aonuma, gave away a few hints as to what Nintendo have planned for Wii U and Nintendo 3DS Zelda games.
Aonuma was equally vague on both fronts, first reminding Game Informer that the Zelda Wii U tech demo at E3 was just that — a tech demo illustrating what a Zelda might look like in high-definition.
In the Wii U’s case, Nintendo are interested in seeing how the system’s power can be used to do things that couldn’t be done before. The Legend of Zelda: Skyward Sword on Wii, Aonuma says, is the first step in illustrating how the series can change.
Then, regarding a 3DS Zelda, Aonuma hinted: "It will be a game in which having 3D will mean something." You can read his complete quote over at Game Informer’s post, linked to above.