Nintendo did not create the d-pad. Intellivision was first there, even before game and watch. All nintendo did was make a cross instead of a disc out of it. And it's not a novel input method anyway, it's just a flat joystick.
Likewise, nintendo did not create the analog joystick in the console space - the atari 5200 had one. In the early 80s. IIRC the vectrex was also analog. Nor did they create the thumbstick - you could attach one to the 7800 dpad, and while digital, it looks almost exactly like an n64 thumbstick.
And while I know of no company before nintendo to have l/r shoulder buttons, they're hardly the first company to have buttons on the top or side of the controller.
They were first to bring force feedback to the home controller, but that still remains a novelty on a d-pad (unlike a racing wheel). One I wouldnt want to get rid of, but a gimmick nonetheless.
So when you peel back the layers, you see that nintendo did not create or innovate most of these ideas. Just popularized them, modified them slightly. They might be the first you remember having a d-pad, but they didn't come up with the idea.
Certainly Sony doesn't deserve the title for anything, but giving nintendo credit for all these things is not quite accurate.