From what I can tell the same buttons exist between Pro and GamePad, so I don't see why they wouldn't be interchangeable, except for games that needed to use the tablet screen.
Please dig out your Gamecube controller and put it next to the 360 controller. Note the stick positions. I would have preferred the Gamecube arrangement, but then people would have really accused Nintendo of stealing the 360 design, having completely forgotten about the Gamecube. I really hope the upward position of RS feels natural, because I still haven't been able to acclimate to PS2/3's double-down.
Hope we get them faster than VC games, I want to play Mario Sunshine and Gauntlet Dark Legacy again.