Aren't the Xbox and Playstation's sticks in opposite positions compared to each other, too? Like, symmetrical sticks for PS, and assymmetrical on Xbox...? That would make it exactly the same as what he's talking about in regards to Wii U's setup, then; muscle-memory being thrown-off 'cos the controller's layout is different. That's just biased silliness.
He's right about Nintendo not supporting the GamePad with the proper game(s) though, like they did with Super Mario 64 and Wii Sports for the N64 control stick and Wiimote, respectively.
I belive he is just talking about the right side of the controller, as in the stick is above the buttons which is the opposite of almost all modern controllers starting with the PS1, N64 gen.
On topic I somewhat agree with him. I find the controllers rather cumbersome and awkward. I would much rather play the games with the pro controller, forget the touch screen. I just dont know how much changing the controller would affect a more casual gamers opinion on buying the system or not. No one seems to know the console even exists.