how about this:
bonus to points added for a win with nations you have played less
and
more points lost if using nations you always use
i think that solves alot. system would have to be worked out but in theory it works.
if you win 100 times with Pythium but never with another then winning with them will not gain u much points at all (even if the opponent is of higher rank.. which would be possible even if he has lost more but uses different races)