the way that i see it is, we're kinda banking on nintendo releasing a wired version of the pro controller, but honestly, that's not unlikely. from now until SSB4's release is a looong time for them to release a type of controller. the four USB ports mean that the same type of play is readily available (1v1 and 2v2s), and it'll be practically the same thing. nothing to worry about.
if any issue is present, it'll be that the Wii U will have to take time to sync the controllers when plugged in, rather than the immediate port recognition we have now, which we'll just have to get over