The 3DS version has Smash Run, which is good single player, and decent multiplayer but it's pretty much the same until the end which is random Smash except VS Enemy Team (which is fun but single player) or Race to the Finish (Awesomesauce and possibly the best part of Smash Run) it also has some good stages, aka Spirit Tracks, Tortimer Island, Golden Plains and Pac-Maze... the Wii U version, though has Classic Controller, Nunchuck and Gamecube controls, 8-Player, Crazy orders, Smash tour..
So I'd say their both good in their own ways.