Nintendo has announced that there will be more cross-platform multiplayer titles with the Wii U, 3DS, and even consoles not created by Nintendo. One is already in the works (PureChess) which will include the feature.
Nintendo wrote:We can confirm that cross-platform functionality is possible in certain titles that play on Nintendo 3DS and Wii U, as well as other video game systems not made by Nintendo. We are committed to helping developers realise the full potential of their software on Nintendo systems