Wii U is generally better, but that doesn't mean the 3DS is bad at all.
Advantages Wii U has over 3DS:
- Better graphics.
- Better controller. The 3DS direction pad can be frustrating at times, and you can en dup doing the wrong moves because of it. You also don't have a C-stick (on the old 3DS). And some techniques are a lot harder to do. Perfect pivoting, for example, is easier on a GC controller.
- More competitive stages. On 3DS there's only four (Yoshi/Lumiose/FD/Battlefield). The others are debatable but most are obviously completely unbalanced.
- Most (big) tournaments use the Wii U, so it's better to practice on it.
- Less online lag. I don't know if this one is true, but it seems like it for me.
- More options in general.
- Kongo Jungle 64, best stage ever hands down.
Advantages the 3DS has over Wii U:
- Portable. This one, while it doesn't affect gameplay, is still huge. You can play at school, in the bus, in the car, in a park, whatever.
- The stages are more fun to play on. While this is not good competitively, it's nice against friends when you just want to have a good time. Magicant is totally broken, but it's still an amazing stage.
That's about it. They're both basically the same game, so the differences are not THAT big. The Wii U is the better of the two if you have the choice, but the 3DS one is still a solid game. The 3DS version might be slightly more casual-oriented than the Wii U.