Hmm taking into account game settings might be useful, id have to tip my hat to someone who can win a 5 player large galaxy match as that would take some skill indeed. Although less impressive, it is still an achievement to win a small galaxy 1 on 1 match to
The experience points accumulated during the game are not really useful at all from the perspective of setting up a ladder system so they shouldnt be taken into account. Especially since any points accumulated would be lost if you changed your empire in every game (or tweaked it significantly). i cant speak for everyone but i know that i usually tweak my empire stats to cater for varying game settings (intel/no intel, etc).
Empire experience points could also be artificially inflated by simply playing a few single player matches against the AI using that same empire file