It's an interesting question that I'm really interested in, interesting.
Since SSB is 4 player local the second screen on the Wii U can't be used apart from mirroring the TV. However SSB as of recently has started to make huge epic single player gameplay so maybe for the campaign the second screen will be used in an awesome way. If that is the case, I could see the 3DS version being the Wii U campaign with cross-save and then having its own multiplayer "element."
Or if both versions are fairly similar, I'd just prefer the 3DS to have a 1 to 1 port. Contrary to popular belief PSASBR is great having it on both a home console and a handheld so this would be better than the 3DS getting an inferior version.