the point is that run is left of jump, or In the case of snes top-left. its a formula that is copied in any game worth a damn, which is why its intuitive to most gamers of that era.
Take a look at the Gamecube version of the Mega Man Collections to see how counter intuitive it is to reverse those controls. Its like they programmed the game with only xbox in mind, where A (left button) is shoot and B is jump (right button) thus leaving the GCN version damn near unplayable because Nintendo kept their traditional B on the left, A on the right layout. It was like a slap in the face to players like me who grew up on NES Mega Man.
But A and B were on a horizontal plane on the NES controller. The GameCube just mimicked that with its button layout.
you're missing the point. In the Gamecube version of Mega Man collections, B was now jump and A was to shoot. The game played so awkward I gave it up for awhile and it took me a while to try it out again because damn if I'd let all that money go to waste. It was just incredibly counter intuitive to someone like me, who has played every single MM game on the NES and then SNES. It became almost impossible to hold a charge shot and jump at the same time because my thumb would end up losing its hold on the A button while trying to press down on B. With the original set-up, and the way it played on the X-box version of the game, you can easily rest your thumb on "A" while it's on the left and apply pressure to 'B" when it was on the right at the same time, which is necessary for this type of game. Once that was flipped for the GCN version, it played horribly.
And the switch from B = run to Y = run in the SNES era Mario bros wasn't a big deal because it still had that same intuitive feel; youcan hold down Y the same way you held B on NES, throughout the entire damn game without letting up and without it affecting your ability to hit the jump button - obviously important for the games design.
I don't know how that seems to trip you up so much, I'm pretty sure it was incredibly easy for any other Nintendo player here unless you never played one growing up and tried it later. Even still, the design of the controller wasn't something as seemingly complex as say the N64 or GCN controllers
appear to be at first sight. Nintendo could of very well labeled left as B, down as A, kept X on top and put Y on the right and players wouldn't of noticed a difference in playing NES Mario vs SNES Mario because mentally nothings changed, only the position of your thumb; which is a much more comfortable position than the NES position to be honest. They only kept B/A on the bottom for traditions sake. It was like "hey look, this a more advanced NES. We've redesigned the controller to fit more comfortably in your hands and added a few extra buttons".
At the end of the day the button names don't matter, its button mapping that does. So even if Nintendo labeled the SNES pad like the X-box pad, Mario would play the same damn way and you'd still be complaining that that "switched everything around". One last thing; if Nintendo did label the button layout the way you wanted them, the X-box controller you're playing today wouldn't be the same, it would be labeled the way SNES actually is. Copy-right stuff I'm sure.