It was never the intention. They've had different stages from the start. There's communication between the two, but no cross-play.
http://www.ign.com/articles/2012/04/26/change-coming-to-super-smash-bros-wii-u-3ds
"As you noted, there is a certain dead end we come to if we just expand the volume of the game," Sakurai told me in a recent e-mail interview, clearly recognizing that simply adding more characters, items and stages wouldn't be enough. The Smash Bros. franchise, though repeatedly earning high praise from critics over its three entries, has effectively followed the same formula since its inception, evolving its style of play without shaking things up too much. So if merely expanding the idea isn't the only thing on Sakurai's mind... what is?
"I intend to change direction a little as we go," Sakurai said, indicating his desire to possbily find a new mechanic or idea to drive two new entries in the series. "The key to that's going to be its dual support for 3DS/Wii U."
So.. what? We're back to simply adding more characters? How exactly is releasing a similar game on 3DS "the key" to avoiding the dead end in terms of gameplay mechanics?
So you want the 3DS version to hold back the Wii U one even more?, I'm so glad Sakurai didn't go the PASBR way with this one.
After brawl, after finding out that namco is playing a big part in development, I'm barely interested in the game at all. No, I'd rather it not be held back.. but that's basically happening anyway (same combat system, right?). Cross-play wasn't what hurt PASBR, either.