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.
I thought Geneology did a pretty good job with how it handled it and it wasn't treated as a good thing either. I think Kaga leaving really brought the story quality down and Fates made it worse with their weird fetish shit.