Using your right hand for the fire button is more important when you have more than one button. With just one button, your left thumb is more than adequate, and gives you greater control over movement by using your right thumb on the D-pad.
Exactly. 2600 games require more precise movement control than button-mashers. I've found when I try to use left-handed-D-pads for 2600 games (the Activition Anthologies, for example), it's like trying to control the game with my elbow or something. I've even tried playing cross-handed, but that doesn't work. 26 years of muscle memory is difficult to overcome.
That's a pretty standard setup that just about all companies use, right from the original Gameboy's and up, left dpad, right buttons.
I understand. The product has to be made to appeal to the masses. Greatest common denominator and all that.
A flippable Lynx-like setup sure would have been nice, though.