Probably the reason why the left handed joystick became the norm was because the left handed pad became the norm. Nintendo was an industry leader, and monkey see monkey do. Street Fighter had in the Arcades a "Left Vs. Right" machine. unfortunately, they couldn't duplicate it at home, because Joysticks tended to be diagonally cocked for better contour, Both the Genesis and SNES had that angle in the buttons, and rotating it 180 would require a left/right switch, and more importantly give a "back-cock" on the wrist, which is even more painful than crossing arms or just playing left handed. (By the way left handed joysticks are not painful, they are just less accurate to those who prefer Joystick right. See above story on how not only I but others of our friends beat my famous gaming friend when they used a right handed stick and he was on his pad. I was pulling off dragon punches left and right, never missing. before I had a 90% misfire rate on a dragon punch, unless I telegraphed it my making 3 distinct motions, then he just blocked So the reason I beat him was improved execution rate and speed of specials.) If you tried that with a more contoured joystick, it would both be back cocked and "smile" at you, instead of "frown" which is a normal button contour.
So when they decided to release Street fighter sticks, making it right handed would be swimming against the stream. But some people like me are Salmons. It all stems back to the Nintendo decision to make right handed pads.
But why was that decision made initially? I have 2 pieces of evidence why the NES pad was stick-left,depsite the fact that Atari defaulted stick-right. The first answer was with their game and watch, where on their patent drawing for a d-pad on a game and watch, the control was originally right handed. need proof? visit http://metopal.com/2012/01/02/nes-patents/ and scroll down until you see the first game and watch drawing. It was originally right handed.
So why did the NES pad become left-handed when the original design was right handed? Because their 4 greatest arcade hits to that point were Donkey Kong, Donkey Kong Junior, Popeye, and Mario Bros. And all of THOSE were left handed. And they figured to play their games on a joypad that would be the easiest thing to do.
But why was Donkey Kong left handed? Because Donkey Kong started as a way to recycle Radaarscope machines.
What's Radarscope? A typical, forgettable (at least compared to Donkey Kong) vertical shooter. That's why the screen was vertical. And the reason why it was left handed was most people thought to put the most important and time sensitive control in the right hand. And people thoguht rapidly pressing fire meant the right hand should be fire, so the right hand was fire. Shooters that required rapid fire tended to be opposite the rest of games. When there was only one player at a time and 2 or less buttons, some arcade makers graciously game buttons on both sides of the joystick. Some arcade owners added it too and advertised it as a feature. But most didn't touch Donkey kong beause of poor coordination in scurrying up the ladders which woiuld throw off many people, eating their quarters, making shorter games and more money per hour. That's why, back in the day, I was better at Colecovision Donkey Kong than Arcade Donkey Kong, because of the left hand coordination of scurrying up the ladders in the arcade vs either hand in the Colecovision days.
As to why the initial release of the Nintendo NES control pad wasn't flippable for ambidexterity, I don't know. Maybe the L/R switch and the wiring was too much. Also Sega stumbled upon another reason when they made their right handed joystick, even though they made left handed pads. How to remap the buttons. Sega thoght their games would make more sense if the left button stayed on the left and the right stayed on the right. I know of 2 games in my collection where that would work: Tuthankham, and Pac-land, where they have fire left and fire right buttons, and run left and run right buttons, respectively. In those games, that mapping makes sense. However in most of their arcade style games, the concept of left and right is irrelevant, and the concept of main fire and auxiliary fire was FAR more important, and the main fire you wanted on your index finger, left or right handed, especially when your rapid firing. So the button would have to be swapped relative to left and right to make sense relative to the index finger. Probably Nintendo saw that problem on the horizon and didn't want to touch it. So they picked a side, stuck with it, and that's how history goes, leaving all Atari 2600 and other right-hand joystick players discombobulated. I still feel awkward playing with a Master System joystick with the rapid fire on the middle finger.
Ironically, it took an unauthorized device maker Beeshu to make ambidextrous and right handed joysticks. But Nintendo said to avoid those like the plague or else your warrantee would be voided. I don't know if Beeshu applied for a license for NES or SMS (if they even thought of accessory licensing, because Sega was making 95% of Master System games. It was a sinking ship in the US, but it was THEIR sinking ship. In Europe, it did well. In Brazil it so dominated like the NES in the US, that over there, it outlasted the Dreamcast.) and got rejected because it was seen as competing, or whether Beeshu wanted all the money to themselves, but they did get a license to make one model for Turbo Grafx 16, and I have a version of that joystick, and that joystick is the smoothest 2 button joystick I've ever played. And of couuse, it's ambidextrous. (But Pac-Land won't work right with the left buttons.)
Does Nintendo still honor NES warrantees. If not, enjoy a Beeshu joystick. What is Nintendo going to do, not honor a long-expired warrantee?