Problems with the scoring system:
A domination against 1 Civ on a small map is worth as much as a domination against 12 civs on a huge map ... the latter is obviously considerably harder, but there's nothing built into the system to accomodate for this.
The number of civs you are playing against and the world size should have a direct effect on the resulting score.
Additionally, the current scoring system is heavily slanted towards domination/conquest style games ... it rewards land grabbing and population size in a weighted manner ... try playing a more peaceful game and you'll see your score slipping unless you continually - CONTINUALLY - found and grab new cities throughout the entire game.
Net result? If one style of play rewards more points over another, it stands to reason that if both styles won a game in the same year, the style that emphasizes growth will actually give more points at the end of the day.
Diplomacy and Culture victories are typically scored in the latter part of the game, but by going for these you therefore resign yourself to the fact that a conquest victory could have brought about an earlier win and therefore more points. Again, more emphasis on the warring style of play.
If I want to score big points, I'll go for a conquest victory over 1 opponent on a small map. 'fin.
My style of play, however, is to have as many AI as possible on a HUGE map ... I have, immediately, cut my own wrists ... the game will be longer and my points much lower because of it. Something doesn't add up.