I totally agree. It has bugged me since playing GBA games on the DS. It has always felt more natural to me to use the Y&B instead of B&A. I blame Super Mario World. That was the first SNES game I played and got used to that layout when using 4 buttons. At least with the 3DS I suppose customizable controls could be implemented in a firmware update, it was impossible on the DS.
Anyone remember Mega Man Anniversary Collection for the GameCube? No customizable controls there either, and it was backwards from the way Classic Mega Man was laid out.