At first I was really worried about the pro controller, but I got to use one when playing co-op Super Mario 3d World, and I can see it will be a lot easier to use for smash than I thought. The way the buttons sit lower than most controllers means that, unlike with a SNES controller, the natural place to rest your thumb is in the wedge between X and A (on SNES I always rested my thumb between Y and B). Between X and A is essentially analagous to how most people including me held a GCN controller: thumb resting between Y and A. Then just like on GCN, you just move your finger down, and basically the exact same distance and position, to hit B when you need to do a special move. Just like on GCN there was no reason to ever hit X, on Wii U Pro, there's probably never going to be any reason to hit Y, and if you pretend the buttons you will never use aren't there (Y on Wii U Pro, X on GCN), it's actually the same triangular button lay-out with the very minor advantage that Y on Wii U Pro is further out of the way than X was on GCN.
The Wii U Pro has far better sticks and shoulder buttons than the GCN controller; the only downside is that you have to relearn where to reach for your "c-stick", but reaching up isn't really worse than reaching down and the real lack of precision or grip on the GCN c-stick was something we learned to deal with and was never a good thing. I think we'll come to see it really is the best controller for smash, and the learning curve will probably be a lot smaller than some of you guys might think now. Especially if you've never actually held one, find a chance; I was doubtful until I did, and then it suddenly made sense to me how it was going to work great.