Wow it always occured to me that O is confirm and X is cancel, just because where those two buttons are and they look pretty obviously like O and X. Never knew other versions had different buttons.
Drawbacks of Japanese version:
Square button is a bit stuffy, you can get it A/Sed for free though.
UMD slot could have a gap, if larger than 1.5mm you can get it A/Sed for free.
You need an adapter for the charger.
But after custom firmware, there is no distinct dis/advantage of any version, besides hardware issues.