I had this crazy Idea in which the 3DS version and The Wii U version had a few exclusive characters (3-5) and both can be used in both versions via connection of the consoles. Let's say you want to play as a character and your friend wants to play as a character from your version. You can interchange the characters via 3DS-WII U Connection.
Example (Not necessary true):
3DS Exclusives
Decloned Young Link (OOT3D)
Krom (FE)
Zoroark
Wii U Exclusives
Decloned Toon Link (WW/PH)
Roy (FE)
Gen 6 Pokemon
Example (Not necessary true):
3DS Exclusives
Decloned Young Link (OOT3D)
Krom (FE)
Zoroark
Wii U Exclusives
Decloned Toon Link (WW/PH)
Roy (FE)
Gen 6 Pokemon