In a recent interview, director of Sora Ltd. Masahiro Sakurai, tells Joystiq that the Wii U and 3DS versions will not offer cross-platform play. According to Sakurai the two games will offer completely different stages, which would make it hard for cross-platform play.

Sakurai did confirm the two version will still interact in some way. One way will be the ability to transfer one’s customized character to the Wii U.

Link