After reading up on a few things it actually makes some sense to release the 3DS version first. It hooks everyone into the game with the "lesser" version (lesser used very loosely) and allows them time to really enjoy it. Then when the Wii U version comes out, instead of having to choose between the two games, they can just buy the 2nd one because they've had plenty of time to get the money for it. By then Nintendo will have released some more information talking about the difference in versions that with enough hype could very easily cause a lot of people to jump the bandwagon and get it for the Wii U as well, especially if there is some interconnectivity. And since it'll be around Winter, with luck it'll be released during Christmas to generate a massive load of sales.
It's not the most sound theory but I could see it being pulled off. I just hope they're not shooting themselves in the foot by doing so.