First I want to say that this is a great game and as a dabbler in things Greek the best that I've found that captures the era.
I had a few thoughts, though not being a programmer, I'm not sure how hard they would be to implement:
1) Is there anyway to model rebels and allied relations based on government 'type'? (as opposed to 'hard wired' presets?) As sieges pre-third century were expensive and long it was a common tactic to try to contact sympathetic political partisans on the inside. (Athens generally getting the support of the common people and Sparta that of the Oligarchs)
2) Perhaps a way, aside from garrisons, to manage rebels? Athens on occasion used brutal methods (execution and recolonization) to handle unruly allied states and Sparta in one instance outright destroyed a city. (Plataea)
3) Perhaps I am mistaken but I thought that at the beginning of the Peloponnesian war (The Archidamian campaign) that most of the Chalcidean cities were under Athenian control. (the exception being Potidea).
4) Given that most sieges didn't involve assaulting the walls but rather building circumvallating fortifications should damage to besieging units be reduced in the earlier scenarios? (with the food stockpile, instead of fortification, determining city surrender?)