Let's see: Poochy Dash, Poochy Dash Gold Rush, better handling of Double Yoshi, greater amiibo support, custom patterns for Yoshi, 31 stop motion animated shorts...is there a difference between the 3ds version and the wii u version? I've only beaten the wii u one. I haven't played the 3ds version.
And while I'm at it, Donkey's Wooly Dong.