Controller seems to work perfectly when I use Wii U Gamepad but then I can't save the game in Zelda Wind Waker. But then when I use the Wii U Pro Controller I can save but there are quite a lot of issues. Just stuff like when I use the right thumbstick and I look to the right it goes way faster than when I look to the left. Same for running around there are times when it won't run but just walk with the left thumbstick. For whatever it's worth, it's the same for left side on the left thumbstick. The left is where it starts just walking.

Rest seem to work just fine.

But any help for any setting would be good. As long as it works properly and I can save then I don't mind whether I use the Gamepad or the Pro Controller.