We've spent some extensive time with a 3DS build of Super Smash Bros., and we recently came across one menu that seems to reveal a feature Nintendo hasn't talked about much: You'll be able to use your 3DS as a Smash Bros. controller on Wii U.
We already knew that the game featured connectivity with the Wii U version. Namely, you can transfer your custom-created fighters between the two versions (so all of the power-ups that you earn in Smash Run on 3DS aren't completely wasted once the console version comes out). But if you're really sold on the 3DS as a controller, or you just want to transfer your newfound handheld skills directly over to the big Screen, you'll also be able to connect your 3DS wirelessly to your Wii U and use your 3DS as your controller.
However, pro Smash players on Wii U will likely want to opt for the GameCube controller option. No word on whether there will be an adaptor that lets you play 3DS smash with a full controller, but given the small screen size, that probably wouldn't be the best idea anyway.