Founding colonies is something I've thought would be an interesting mechanic for a long time. Could be introduced as a global mechanic via colonists. Add a better (or simpler) bonus for monopolies, like +5% science & culture empire-wide (as someone above suggested), and perhaps +5 happiness per monopoly. Some bonus to city state allies would be interesting too, synergizing with Statecraft -> Imperialism and also the city state bonuses of Autocracy.
Chuck in a small military supply bonus per puppet and Imperialism strongly incentivizes colonizing, conquering, and allying city states all for the sake of gobbling up as many monopolies as possible to benefit your homeland cities.
Industry could be steered more toward bonuses for cooperation with other civs in order to mitigate overlap with Imperialism.
More of a complicated idea but a WC proposal that punishes puppet ownership would also be interesting.