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.)