An old-timer in the UK once explained that the standard (for everyone except Triumph) of up for down, was originally set up that your hand on the twistgrip and your foot on the gear-shift were going the same way. Same reasoning for having the shifter and the front brake lever on the right - all the speed-control related actions on the same side (well almost!).
The most dangerous version of shifter I ever came across was on a friend's Bridgestone 350. Being Japanese of course, it was left-side shift, but it had a peculiar shift that could go from 6 through N to 1. (N-1-2-3-4-5-6-N-1 etc). It downshifted the other way, too.
What bit him was a shift at about 85 mph, when he thought he was in 5th, changed up, and got what he thought was a missed shift. One more stab on the pedal got 1st. When he released the clutch, the engine tried to go to about 20,000 rpm and locked solid. The bike then went into a slide and pitched him off.
Bike was totaled, he was banged up quite a bit. Later, Bridgestone introduced a shift indicator light that came on in 6th gear, basically to tell you "no more upshifts".