My only complaint about the pro-controller is the placement of the buttons and the right analog stick. They're arbitrarily placed that way for the sole purpose of being different than the Xbox 360 gamepad. It is ergonomic to have the left analog stick and the buttons at the same position towards the top of the pad, which happens to be the default position your thumbs are when your hand lightly holds it, simply because the left analog stick and buttons are the most-used items on a gamepad. Apparently Microsoft is now the only company that has an ergonomically-friendly gamepad design. The GameCube pad was fantastic Nintendo, why the hell are you doing this?
I'm waiting until I get it in my hand, but I see two possible advantages here:
1. That's actually smarter for shooters. You talk about the buttons being where you want your thumbs, but for a lot of those the buttons are secondary to the right stick, you'll use the four on the top more than the four on the face.
2. By keeping the D-Pad and face buttons aligned it may actually be more comfortable than the 360's is for platformers, even if you somehow replaced the 360 D-pad with a good one. That was one of my issues, I can deal with Left stick/Right Stick being asymmetrical, but the D-Pad and face buttons are another story.
Still, I imagine a different shape MIGHT have been better for that specific layout, and I do worry about how the Pro Controller will be for action games like Devil May Cry that don't need the right stick as much as the face buttons. I suspect the 360's layout is going to be best for games like that, 3D Platformers, basically anything where constant camera control isn't necessary.