the supply line system is what I have been craving for in games for such a long time, the moving away from amassing enourmous armies (like in total war) and waltzing over youre opponent becomes a very rare thing to do (unless at later games) just because they'd starve on the way there without proper preparations. this makes tactics on a whole new and realistic level possible.
to make it even better however (and I think this is possible)
- to be able to drill youre troops, they all start out with a few points in something, allow for an initial disposition of strengths (logistics, engineering etc) to mimic the actual drilling of troops.
-to 'offer battle' with a little more response then just skirmishers rushing in and out of the city, like (as already mentioned) a pitched battle with bardilys in the macedonian campaign. you could get a popup saying that the 'macedonians are offering battle at pella' or something in the like. something which was actiually done at the time.
at that point the AI would set up its force and you'd have a battle on youre hands, in stead of the siegefest/skirmishes of the moment.
-make it possible to bribe certain towns, offer terms of truce/alliance and annex territory. the diplomacy is nice but it could go a little more in-depth.
for instance a peace treaty can be broken with a faction when certain pretext present itself. (earthquake/political scandal/divine decree/popular demand) and you should be able to barter traties better (this city for that one, farm for mine etc etc) in this way you could bring a state to its knees with more realistic options then just extracting tribute. and also to force treaty expiration date, so it needs to be remade every 5 years or so, this to make unrealistic peaces void
-annexing a city of a faction whom you are currently at peace with by sheer intimidation (the opposite of revolting)
-make it possible to improve a factions standing to you, by sending gifts/embassies of friendship etc.
This just to improve the best aspect of philips conquest, for his diplomacy(and abuse of it) did far more for him then his armies did to make him hegemon.