I think the 3DS version can have potential to get people interested in the Wii U version if the Wii U version has the right content that makes it irresistible to the 3DS owners who enjoy the game.
What that right content is I can only guess!
Similarly, if the 3DS version plays bad, then it can make new customers who don't want to buy a Wii U and Smash U, and buy a 3DS instead, avoid the Wii U version.
If only Pokemon had a home console and handheld version like Smash Bros : /







