*If* they do use a screen controller and I'm still not 100% sold they will, maybe that patent (and subsequent fakes based on said patent) wasn't soooo far off. The Game Informer editor did say he was told of a controller with no face buttons.
Imagine a free form LCD display "slab" basically, that can attach plastic transparent overlays on top. You could have a Pro Controller style button layout. A GameCube layout. An N64 layout.
Or even beyond that a very different/new controller layout. Plastic overlays would only cost like $1-$2 a pop to mass produce. Nintendo could ship the NX with a standard Pro Controller style overlay, but also with a more unique setup with something new perhaps that interfaces with a touch panel somehow.
Just a thought though.