The main problem with doing it reverse is that you make a game that no one but you can properly play. Left side is direction, right side is buttons has been the standard since 1984, even before then there were not a lot of exceptions other than the Atari 2600 console. It also actually made sense on the 2600 because it only had a single button (see the rules below).
More specifically the real rule is that controls are set up so that the right hand does the fine controlling and the left hand does the simpler control. That is why analog flight controls, trackballs, and one button games all put the directional controls in the right hand.
I suggest putting the joystick in the middle and putting the same buttons on both sides of it, that way when you go to show it off to someone else they will actually be able to play it.
In any case don't bother trying to make a two player machine with the controls reversed, because like I said before, no one else will be able to use the thing but you. I can play Pac-Man or Galaga with right hand on the stick, but as soon as the game wants a second button I am no longer capable of playing it with the reversed controls.