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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?
Faulty premise, I do not consider the right side to be more comfortable. If it were up to me, A would be bottom, and B would be left, because in a lot of games B tends to be attack and A either jump or some dodge roll. That setup makes it convenient to place the thumb over both buttons simultaneously.