For instance, the Civ games are basically Whig History: The Game, presenting liberal capitalism as the ideal end point for all societies. It even includes uncivilized "barbarian tribes" whose sole purpose is to be exterminated so you can take their land for the glory of capitalism.
Yeah, thats an issue with the AC games set later, because the politics of those times still directly effects us. Especially Unity and AC 3. The Ezio games dont have that problem, or Black Flag which is a fun pirate sim.