I can't see micro-transactions working well for Civ. That's more of a mobile/browser game kind of thing.
I don't see it working well for civ either (I don't seriously think they'd go that way), but plenty of PC games have started moving that way with micro transactions/cosmetic upgrades - mostly online focused-games though (i.e. dota, league of legends, cs:go). I don't think there's much appeal on skins on a primarily single-player game (and a lot of those games get much more in the way of free patches/balances).. The Sims had tons of cosmetic DLC, though that was more or less the point of that game, but if they decided to take Civ in a more 'SimEmpire' direction, that's something they could do. For instance, have the base game have the 'regional' building look (as now), but sell civ-specific building/unit graphics as DLC. I don't think it would sell terribly well, though, especially with the amount of mod-able content.