dtgreene: I was just reminded of something else I find unsettling about some of the early Civilization game (including, at least, Civilization 2): The games present Monotheism as an advance over Polytheism. Basically, by making Monotheism a technological advance that comes after Polytheism (and has Polytheism as a prerequisite), the developers seem to imply that Monotheism is superior to Polytheism, a stance which I strongly disagree with.
Caesar.: I think that's looking too much into it. The tech tree is a simplification/abstraction of History, mostly from a Western point of view, and polytheism came before monotheism. It was also that way in Age of Empires.
Actually it goes a tad farther than that. There's an implied hierarchy of values (later is better, benefits people more) that illustrates a naive evolutionist worldview. By naive, I mean commonplace, "common sense", but long dismissed by anthropological science. You are right about the games betraying their cultural origin (which should be expected), and oversimplifying history (even specialists wouldn't be able to model all the causal links between all aspects of societies), but it also shows a system of belief that goes beyond mere facts (such as mere chronological sequences). It implies sequential necessities, hidden mechanisms, causations, etc...
No big deal. They are games, made by game producers, they are not supposed to be avant-garde ethnohistorical treatises. Of course they will echo common beliefs, and, even today, our societies often see themselves through evolutionist lenses. A critical distance to them is obviously needed, just like you have to keep a critical distance towards what supermario teaches you about mushrooms.
The nagging thing, for me, though, is that I started playing these games at a time where I was reading Bernard Werber's third "Ants" novel. In which, a programmer designs some totally accurate Civ-like game, that modelizes our cultural evolutions perfectly, and which AI sims end up realising their conditions and revoluting against the users - making the screen explode at some point, in an attempt to kill their gods. It's not a very good novel (compared to the first "Ants"), but it really, really made me wish for a game that would indeed re-create History as an emerging process. It was a nice dream.
So I was always a bit disappointed to realise how these games just have to follow scripts or codes defined by our own models, assumptions and simplifications. Because of that little Werber romanticism.