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Sega, Xbox, Steam - and functionally speaking, even Sony all default to a face button scheme with the action/enter/accept button on the bottom, and cancel/back on the right. Nintendo's control scheme is really the primary thing that throws a wrench in retro handheld setups. It's also just a bad layout. X on top? What is that nonsense?
Nintendo was first with the NES. And by that I mean that on the NES controller, you have to move your thumb the same direction (counter-clockwise) to get from A to B as you do on the SNES. So I count that as precedent.
But yeah. Your point stands. The rest of the industry just decided to screw up the standard long ago.
(If Nintendo had "A" and "B" buttons on any Game & Watch systems Before the NES, I'm unaware.)