I can't help either V. Amoleo but I'm still gonna add my tuppence about Twilight Princess, if you don't mind.
This is something that will always be with me, that pretty much sold me on how motion controls were a natural progression for gaming (as well as THAT Water Temple boss fight). A while after finishing TP, something possessed me to pop in the GC disc of OoT. I started a new file and was running round the Kokiri Forest, getting the sword and gathering rupees to buy the shield, you all know how it goes.
So, I ran into the grass and this is no lie, I couldn't remember how to swing the sword! Suddenly I realised I was holding a controller and didn't know what to do with it. I shook it instinctively but nothing happened. I really had to sit and think for a minute what to do!
Even with Twilight Princess simply being waggle controls, it had ingrained itself on me and I missed it. (I worked out the OoT controls and got near the end of it on that file before being distracted with something else.)
Fast forward and similar things have happened to me with the 3DS. I think I also did some stupid things that I carried over from SS to OoT 3D as well as shaking the thing in an attempt to make Mario spin in 3DL, as he did in the Galaxy titles.