For those still on the fence about which version to get (at least between Wii U and 3DS), I'd recommend the Wii U version. I've played both extensively at this point, and while the stereoscopic 3D in the 3DS version does look really great, the way StreetPass is implemented in Shovel Knight isn't all that compelling in my opinion. Plus, a lot of people don't like the 3DS's 3D, and without it on, the game looks significantly worse on the 3DS's low-res screen than it does in HD on the Wii U.
Seeing the fantastic pixel art on a big, beautiful HD screen and having the stupidly awesome Kaufman/Matsumae chip music soundtrack pumped into your ears via legit speakers just takes the already great Shovel Knight experience to a whole new level entirely.
Plus, the Wii U Pro Controller is quite easily the best official controller to play Shovel Knight with. It feels perfectly good on 3DS and on the Wii U GamePad, but the Pro Controller is the way to go if you can swing it.
That said, I did find relic selection to be most convenient via the 3DS's touch screen, but that's not enough of an advantage to recommend the 3DS version more than the Wii U one in my opinion.
Go Wii U if you can. Otherwise, the game is fantastic on any platform you can play it on, so you can't go wrong either way.
