There are four things I hate about the Pro Controller.
1. I find the analog sticks way too slippery compared to Playstation analog sticks. (This applies to the GCN's analog stick as well).
2. Trying to grip the handles hurts my hands, so it only works well for having it rest on my hands which is really annoying compared to the GCN controller's grips and the Classic Controller Pro's grips.
3. I absolutely hate the placement of the ABXY buttons and the dpad, but the dpad isn't very important in this game.
4. Not a fan of the digital triggers. Well made analog triggers are way nicer. However, there are no real benefit to analog triggers in this game and they shoulder buttons work way better for Smash 4 than the GCN controller's shoulder buttons.
Despite my complaints, I vastly prefer the Wii U Pro Controller over the GCN Controller for Smash Bros. The analog sticks are a vast improvements over the GCN analog sticks and I replaced my Pro Controller analog sticks with DualShock 4 analog sticks. The ABXY buttons interface works much better for me with this game because of my button configuration where A = Smash, B = Jump, Y = Special, and X = Grab. The digital shoulder buttons also reduce any delay I would get with a GCN controller.