Currently, the 3DS version has an advantage over the Wii U version, from my understanding: The Street Pass battle mode, and 3D support (though the game still plays the same, it shows up in 3D, making things look better from my understanding (I don't have the 3DS version, so I can't confirm how good it is myself)). However, the Shovel Knight amiibo is going to give the Wii U version a co-op mode...
09/26/2015 1:16 PM
...and will, from my understanding, unlock extra challenges in both the 3DS and Wii U versions of the game. At that point, I think it will become a matter of preference.