note: I jotted down some similar thoughts a while ago somewhere (I think before the glorious disappointment of Civ5 came out, actually). Hope i can find them and also upload them, on the (currently low) hope that further iterations of the game will pick up the lost-hope of ever-improving real-world simulation games.
Civ4 is a good simulation (and learning tool) for: global international relations and diplomacy/espionage, the effects of balancing government spending on the military vs. the economy, culture, and technology, as well as the importance and use of basic strategic and economic resources
(advanced game): Importance of trade, essentiality of espionage, (with AI: importance of trade, shared culture/religion/civicvalues on relations)
marginal representation on: religion, culture, modeling of modern governments and relations (both diplomatic and commercial/extragovernmental).
important omissions noticed: oil logistics (pipelines), internet revolutions, drones, drugs, canals, effects of internal politics (clan wars?), effects of gov't on media and vice-versa.