I'm not about to get into an argument about which version is better, but there are no doubt advantages to both choices. It's simple really, you just need to decide what is most important to you.
Do you prefer portability with a focus on single player? Then I would suggest going with the 3DS version.
Or do you favor more powerful graphics, easily accessible multiplayer, and a greater variety of controller options? If so, I would definitely suggest going with the Wii U.
Personally, I wish I could get both versions, but it simply can't be done at this time. I decided to go with the Wii U because it is definitely a Smashbros experience that I'm most used to. This way it is much easier for all my friends to get together and play around a big TV you know? It is also most likely going to be the tournament standard especially due to the GameCube controllers coming back.
What matters to you the most?