Mainly the patent explicitly saying that software would be scaled in performance based on the form factor that said software is being played on. There's also the fact that Nintendo can't support separate console & handheld platforms without software droughts, anymore (especially with mobile gaming now becoming a thing at Nintendo).
I get this, and it's to be expected, but does this patent specifically apply to NX? Or is it just something that came out of Nintendo and was applied by observers to NX? Iwata sounded like NX is intended to be something 'totally new' and mass market, another Wii if you will, which doesn't sound like it would apply to a dual format model if some fancy interface is involved. If NX's big surprise feature scales with software/hardware too, it would be huge commitment, but maybe a wise one if the surprise is as good as Iwata hinted at.
It's super weird to say this about a person you've never met. We literally have no idea about his internal state. For all you know he hates and resents the company and only stays out of a sense of obligation. Not saying it's likely, just saying we can't infer anything.
How do you know I haven't met him? Even if I hadn't, It'd be very easy to get a picture of where he's at professionally speaking from his work and the many, many interviews he's given. The idea that he resents Nintendo, even hypothetically, is remote in the extreme. He could have moved in many career directions should he have chosen to -even outside of videogames- based on his reputation alone, but he's stayed with Nintendo because that's clearly where he's happiest.
Yamauchi and Howard Lincoln both considered themselves part of Nintendo after they retired/left, and I wouldn't be surprised if Miyamoto felt the same.