It's hard to have a rating system which takes server differences into account. One possible way would be to have a server rating factor, and assume that if 2 ppl with the same colored name are playing in 2 different servers, then it's the same person, so their rating must be the same in both servers, for example:

EtplayerX plays on jaymod and he owns making scores 2 times better than the rest, then he plays with the same name in some etpro server and he gets his behind kicked, then the factor for that server would go up and the other down, with players getting a lower rating there. Eventually his points will become equal in both servers due to that factor.

I guess there would be lots of whining then plus you can't be sure if 2 different people are playing with the same name...

Anyway the difference in difficulty between different servers doesn't lie much in the mod used, but mainly in the players who are regulars there, and server settings which suit the taste of beginners or more experienced players, plus some unwritten rules in some servers (like, if one is a total noob he will be sometimes voted for kick, then the average server skill goes obviously up).

In my opinion it's all about this: you set the rules and the score for a game, then players will obviously figure out how they can get a higher score, and the solution could even be playing against people who are worse.
I think that stopping xpwhores and comparing points vs teammates only would be already a huge step forward. For the rest, it's a game, who is able to play better *that* game will get more points. That doesn't mean they can do better at other 'games' but if it takes skill, skill is still skill.

@giriel:
well for the other formula, (the one with kills/deats) the problem is that scores can skyrocket if someone manages to have only 1 or 2 deaths, let alone 0, it would be a division by 0.
If I collect some more data with /statsall I could try other formulas myself, but I am sure that you know what you're doing