The only way I can see exclusive characters happening is if they're just different versions of the same character. Example: Toon Link and Classic Link, or Young Link. Skyward Sword Link and Ocarina of Time Link. Classic Sonic and Modern Sonic (Generations style). Melee Roy and Awakening Roy. Classic Wario and Biker Wario. Possibly Mario and Doc? Exceptions could be something like Sheik and Impa, who, while different characters, could play the same. This way the roster doesn't change and the moves wouldn't either.
Each system would, if possible, get the version of the character who has appeared on that system or type of system; therefore, the Wii U version would have Toon Link due to WWHD, while the 3DS version would have Classic or Young Link due to ALttP2 or OoT3D respectively. Wii U would get SS Link due to SS being on the U's predecessor, while the 3DS would get OoT Link due to, again, OoT3D. Wii U would get Melee Roy because Melee was on the GameCube, while 3DS would get Awakening Roy due to Awakening being on the 3DS.
The Wii U/3DS connectivity would then, in addition to any potential customization, involve getting those different versions of the same character into both versions of the game. Additionally, perhaps you could play against Wii U players on your 3DS or vice versa? That might not be feasible though.