I am not gonna get the Wii U version. The only reason I would play it would be if a friend gets it, or if my family gets a Wii U, and Smash will be the only game I would want to play on that console. 3DS is what I am sticking with, and I would rather play it on that than a Wii U. This is only my preference, and I don't believe that it is the right way to look at it.
That being said, I would like to say that neither version is gonna be better than the other. Sure, one has this, and the other has that, but this is all opinion. The 3DS will have more people using it, but the Wii U is more of a party game (there are other stuff too, but I am too lazy to write it all). Also, lets say money doesn't matter. It just depends on what you want.
It could be how your life is. If you are usually away from your house, the 3DS would be a better fit. If you are usually at home, the Wii U would be better. I don't see why graphics are much of a problem. It never seems to come up in a Melee VS Brawl argument, so why bring it up here?