There will be a brief diversion at launch with tournaments (get togethers, really) strictly based just on who has which version, but eventually the 3DS players will have to migrate if they want to play, whether they like it or not. Interest in the 3DS scene will wane. The Wii U version is just much more convenient in every way. In terms of community success, you may as well consider the 3DS Smash the Super Street Fighter IV 3D Edition. 3DS owners may outnumber Wii U owners 10:1, but that is subject to change. The Wii U has several more quarters of sales to push the console, and more people are committed to buying the Wii U and software as exclusive titles are approaching launch. BaPr's poll is highly insubstantiave, but if it reflects remotely reflects the system demographic, then the great majority of community smashers will very probably be Wii U owners.
I honestly don't see this splitting the community, and especially tournaments. Most actual competitive players see the console option for a game as a no-brainer. In terms of what most players like to experience in Smash, I don't see either version being so different at launch as to warrant splitting the casual scene. It's hard to imagine them giving that big of a crap.