I know this is an old topic, but grave digging is preferred over duplicate threads, isn't it?
Anyway, I just wanted to say, that I do think that both versions of the game having the same roster was a bad idea. A prime example of this is the fact that the Ice Climbers were cut from both versions of the game because they were unable to work on the 3DS. So, the Wii U's roster is limited by what the 3DS can do. That sucks. The Wii U version should be able to push itself as much as it can, just like Melee did on the GameCube and Brawl on Wii.
The 3DS version could have focused more on characters from handheld games and the Wii U version on console games. They could both have the same core group of characters (Mario, Link, Fox, Falcon, etc.) but have some characters different, to individualize the games further. So you could have, say, Isaac in the 3DS version and Wii Fit Trainer in the Wii U version, just for an example.
I've seen some people here say that having a different roster for the two different versions of the game would be bad, but that's how it usually goes. Obviously, the n64, GameCube and Wii versions all have different rosters and nobody's complaining about that. More games should mean more rosters. How excited would you have been for Brawl if it had the exact same roster as Melee? Granted Melee's roster was pretty good, but still, we always want more characters, right?