They've stated time and again that ice climbers and transformations didn't work on the 3DS, which is the biggest reason they were cut/separated.
On top of that, the games aren't even "the same" as they've claimed they wanted them to be, as nerfs/buffs are missing on the wii u version, as well as some chars just plain functioning differently (a prime example of this that I've noticed is Jigglypuff. Her bair comes out much faster on the 3DS version, and she can't run into people laying on the ground and rest them on 3DS, where it's far far easier on the wii u).