On one hand clearly its easier to get a conquest victory on a tiny map, on the other hand any old joe can milk a larger map until 2050 and get a large score just from settling cities and sheer population. So how do you fix the scoring so that both are equalized?
Basically they are on two different poles, conquest is best for small maps, and building is best for large maps. You would have to have two separate scoring systems, one for conquest and one for milking the game. The conquest one would give more bonus for larger maps, and the other would give more bonus for small maps.
Giving a bonus for smaller maps on the basic population scoring system should equalize the scores between a tiny map and a huge map. So those of equal skill would get the same score no matter what map they played, they wouldn't get a bonus just because the landmass supports more cities and therefore more population which creates higher scores.
Same could goes for conquest, on a tiny map if the best my skills can muster is a 200BC win, and on a huge map if the best I can do is 1500AD, the score I should get for both those games would be similar in a balanced scoring system.
The only thing I think may be a good idea that we as players can do is just create a balancing factor for the game size and type. For instance I would make medium the standard map size and its factor would be 1.00, tiny for conquest would get maybe something like 0.50, whereas large would get 1.5 (just guesses, I doubt tiny and huge are equally distant from medium scores).
On an unrelated topic:
Duke,
Kind of a rules clarification, when you say default rules would that include something like specifing which other civs you are playing, or how many? I noticed the winner in the chieftain level turned off 2 of the civs so that he only had to defeat 1 civ in the game. That doesn't seem very fair, and also potentially ruins it for conquests, since its obviously easier to conquest when you only have 1 enemy, right? This can be said about non-conquest games as well less civs less competition for land.