This feature, as well as the ability to transfer custom fighters, is the only connectivity the two versions of Super Smash Bros. will have.
Japanese gamers have been playing the 3DS version of Super Smash Bros. this week and have all but confirmed all the secret characters. But, GameStop has revealed a different kind of feature, namely, what the "connectivity" between the 3DS and Wii U versions of the games will consist of. It looks like 3DS gamers will be able to transfer custom character data, and use their 3DS unit as a controller for the Wii U version of the game.
Earlier, game director Masahiro Sakurai did confirm that the two versions would not be able to play together directly, but did not outline what the connectivity options would be. The transfer of custom fighters most likely refers to the custom-Mii fighters, as well as regular fighters customized with power-ups earned in the 3DS-exclusive "Smash Run" mode.
I suppose the good news is that players who hone their skills using the 3DS's control scheme ahead of the Wii U launch will be able to show of those skills on the big screen, and it would also help out new Wii U owners that haven't shelled out for four controllers yet.
However, I can't imagine many Smash Bros. veterans would opt for this option over the GameCube controller adapter.