But in which direction will my thumbs "naturally" point when I rest my hands on the device? If I've been playing a lot of Xbox 360, my thumbs will "naturally" point in a somewhat different direction than if I've been playing a lot of PlayStation 3. And different people's thumbs are different sizes. Furthermore, hands will shift somewhat during gameplay.
The direction your thumbs point doesn't matter, as the iPad doesn't calculate the orientation of your fingers, merely where on screen they touch. If you want to put them on a 45 degree angle, that's fine. Naturally, up is still going to be towards the top of the screen, but with the bevel as a sort of guide this isn't difficult to maintain without looking at all.
Are you talking about the system described here and used for directional control in Super Mario 64 DS (2004), where the thumbstick recenters each time the thumb is lifted and replaced? If so, how easily do players adapt to "right thumb swipe up == jump"?
I don't play a lot of games, so I can't really say what the typical scenario is. However, from the ones I have which have some sort of "jump" feature, this is usually given a dedicated button, with the virtual gamepad acting more for direction than discrete actions. Different control surface requires a different input paradigm.
The best games also provide a system whereby when plugged into a TV or connected wirelessly to an external display they display their gaming graphics on the external display, and the entire mobile device becomes nothing but status information and the control surface. Really quite slick.
Was this before the Wii U was first publicly demonstrated?
This functionality was demonstrated at the iPad 2 launch on March 2nd, 2011. According to Wikipedia, the Wii U was first announced in April 2011. So it seems like it was indeed.