A complete rework of the culture mechanic. At the very least, provide the functionality of the EU3 culture mechanic, with primary & accepted cultures, culture groups etc. instead of the wonky thing we currently have.
Ideally, there would be cultural policies/decisions or some kind of relationship matrix for the cultures in your empire, so e.g. you could decide to increase relations with the Persian subject population, maybe even make them an "accepted" culture, but at the cost of angering your Macedonian core population.