There's an easy way to 'patch' all this. Fix the PR system. Give less and less point for the civs that have the higher win percentages. People chase PR like it's some kind of gold mine at the end of the rainbow. Imagine if you enter a 1v1 spain vs japan and you're japan and you stand to lose .25 full pr and only gain .0003 if you win. Granted, you'd still have to take into account rank and HC level and all that jazz, but it'd solve the problem.
That's the best idea I've heard from anyone in a while.
Granted the civ still needs some serious nerfing either way because Japan can be even worse in team games since it has more time to work with. However, your exactly right with the PR thing.
NO, please no. If japanese dudes my rank can beat me without breaking a sweat will not increase rank that means I'll ALWAYS face the same japanese dudes over and over again. If it went faster, I'd start facing either guys who are not overrated or jap lamers that suck. The second option looks better.