Having used a WiiU the other day and owning a 360/PS3, the verdict is still the same. The 360 simply has the best controller i've ever used. The gamecube controller was awesome, but is too small now that i have big hairy manly hands.
The WiiU pro controller is weird, because it's much more natural to flick your thumb up and to the side off the stick to hit the face buttons, than it is to push your thumb down and across. Try it now without holding anything and you'll be able to feel what i'm talking about - switching from aiming to the face buttons on the 360 feels sorta like a thumbs up, natural and quick, while doing it in reverse - while not bad - isn't as smooth.
The 360 one also has the face buttons on the right angle for that movement and have a perfect texture for it.
The best way to see how the WiiU pro is wrong is to imagine trying to hit 'A' quickly after using the stick. See the problem? Now with a 360 controller, look at the closest buttons to the stick and it's easy to hit them fast.
The dualshock controller is just not as good overall. It has the benefit of the 'flick-up' thumb thing, but it's not as ergonomic and while the pressure sensitive buttons sound good in theory, playing a game that relies on them is an effort in frustration, while the triggers are completely shit.
I prefer the dualshock for fighting games and RPGs, though, with the better d-pad and big face buttons.
All of the those controllers, however, are superior to the standard WiiU screen gamepad, which is shit in so many different ways it's incredible.