Taken from the latest Gameinformer Magazine on the game:
“Nintendo is planning on bringing Fox Mcloud out of retirement for a new entry on the Wii U. Fox will be able to fly his Arwing and seamlessly transform into a tank during certian sequences. Pilots can control the game either with their Gamepad’s analog sticks or motion control. The game was very early in development and looked admittedly rought the last we saw of it, but we’re hoping Fox gets the new, grand adventure he deserves.”
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It certainly seemed like this would be the case as Nintendo has been giving lots of control options in it's games as of late with the Wii U and all it's controllers. This is a nice confirmation that motion controls with the Gamepad will not be forced on the players.