There are only a handful of cities like Pydna that are converted from enemy cities to native macedonian after completing certain objectives (usually after moving philip there). These are based on historically colonized cities so it won't happen just anywhere.

There are also cities (like larissa) that become "allied" with macedonia as a result of some objectives and these won't rebel but still build mercenary units.

One other way to prevent rebellions is to tear down a city's wall. Historically this would limit rebellions as the city had no way to defend itself against its captors. Also, the size of force required to keep down rebellions is based on the faction's hostility so it will be harder to hold chalcidian cities vs paeonian ones.

Finally, if you haven't tried it yet, Hegemony Gold (which is in beta and currently free to try for anybody who has bought Philip) significantly changes the population system and introduces alliances and allied units which you might find interesting.