Ergonomics aside my main gripe with the Wii U GamePad is the short battery life and I have the official extended capacity battery installed. I can get about 5 hours of play time in between charges and that's not good. The normal battery gives me around 3 hours of play time. A typical gaming session may last me up to 4 hours and if I'm feeling extra adventurous, I'll go through an all-nighter.
With the Wii U Pro Controller those 12-15 hour sessions are absolutely no problem and my hands do not suffer from fatigue like with the Wii U GamePad after just 30 minutes of play time. Especially with the extended capacity battery as that makes it heavier. I'm also faster with the Wii U Pro Controller. Everything feels closer and my thumbs rest on the analog sticks at a much more comfortable angle. I very much have made it a requirement for a game to support the Wii U Pro Controller now as otherwise I'll skip it. It's that much better than the Wii U GamePad. Never have and never will use any of the second screen enhancements. I only ever try them for 15 minutes in games that make use of the Wii U GamePad, after which I just switch the controller to the Wii U Pro Controller.
I rest my case.