The only problem I see happening is the roster screen for the 3ds. I think DLC will happen for it on the Wii u release but its easier to change the roster menu on the Wii u because of the size of the screen
The Wii U version would actually be more limited on space for the roster because four people will have to be able to access the whole roster at once. There will only be one person on each 3DS so just like @
Skyblade12
mentioned, they could just make the 3DS version css scrollable.
Personally I'm quite disappointed that the Wii U roster is limited by what the 3DS could handle, otherwise the Wii U version could have really gone all out. Uhm... I guess the 3DS version could get some DLC character when the Wii U version releases. I mean, it's Nintendo so you never know what they'll do. But, as long as the Wii U and 3DS rosters are the same, they still can't add any characters that won't work on 3DS for whatever reason.