I've been playing this game like crazy the last few days/weeks. It's that much fun.
I'd like to put forth some ideas, though.
1. Population - Maybe the population number for cities should be more dynamic... Like, instead of using migrants or colonists to solely increase your effective population, it should naturally grow on it's own, though gradually. Bigger cities should logically grow faster than smaller cities. But say, another city has reached it's maximum population, you could branch off a unit of effective population to create colonists/migrants to send to a smaller city to bulk up it's smaller population/reproductive rate.
Each population number should also represent a full bar of recruits, so if you lose the entire army from one city, instead of just losing the temporary recruits number, you could lose a unit of effective population as well.
Maybe you could also have a button to convert a unit of effective population into recruits? I dunno what this would do for balance reasons, though.
2. Enslavement and Razing - In complementing this new idea of dynamic population, you should also have new decisions for dealing with conquered cities. Either for personal or strategic reasons, you could force some or all of a conquered city's population into slaves. Or you could simply turn their entire population into migrants, and send them to other cities.
Another decision for conquered cities, again, either for personal or strategic reasons, should be the ability to "raze" a city. Where you loot the city of it's population and food, leaving behind an unpopulated ruin. Now of course, the enlightened conqueror might not think this wise, but say there's an enemy you just can't fully deal with at the moment, so you raze a city or two to raise intimidation, and focus their efforts on rebuilding that city instead. Both Philip and Alexander did this a couple times.
3. Culture - This is kind of covered by the "native population" element of the city, but I'm thinking the culture of a city should actually be listed on the city screen... Something like " Culture: Macedonian ", and then tying unit trees to that instead. So now, you can actually alter the population/culture of cities around the map. So if you wipe out the population of a Pherean or Chalcidian city, you could replace it with migrants from one of your Macedonian culture cities to give that city a Macedonian culture. Or vice versa.
That's all I can remember for now. This is a wonderful game, and I would like to thank the makers so very much for it. I guess I should get back to playing it now.