Sakurai said that the Ice Climbers were working in the Wii U build of the game, but were cut because they couldn't work on the 3DS.
For many Smash Bros. fans, the leak of the full roster was a moment of joy, so many new faces and returning favorites to look forward to playing on release. But, for some fans, namely, those who used Snake, Wolf, Lucas or the Ice Climbers as their mains, it was a day of sadness to discover that they didn't make the cut. Now, game director Masahiro Sakurai has explained why at least one of these fighters, the Ice Climbers, were cut from the game, and it basically boils down to: the 3DS version couldn't handle them.
Sakurai told Famitsu that the twins were actually playable in the Wii U version at some point, but due to the 3DS's limited hardware power, the team couldn't make them work in the handheld version. He also said that the Ice Climbers didn't have as high priority as many other characters, as their series wasn't likely to see a new title in the foreseeable future.
In the same interview, Sakurai talks about why the release dates for the 3DS and Wii U versions were split up. He claims that this was due to debugging for both games being done separately due to their considerable differences, and if they had aimed for a "combined launch," we probably would have been looking at 2015.
Either way, this really sucks that the characters were working on Wii U, but were cut due to the 3DS - it's definitely a case of one version of the game holding back the other. Would it really be such a problem to have a couple of characters exclusive to the Wii U version?