morale, supply lines, reserves. i was thinkin about that stuff not too long ago. glad to see somebody could incorporate them into a mod. some other ideas to ponder:
propaganda
mercenaries. available in various random cities (foreign and local)
slaves (sort of draftees without pay)
reincorporating firepower
the ability to band together a stack of units into a cohesive fighting force (army) using a general which would be created early on by the palace and later also by war academies. the number of generals would be determined by the size of your civ. the stack army would have the advantage of attacking and defending against another army with each unit being preplaced in battle (front line, in reserve, or in rear). units in reserve could move up to replace fallen units or have the option of flanking the outside units. bombarding units like archers or catapults would typically stand to the rear and reign hell on selected units.
instead of building units, conscript and train them. using a barracks or a palace you could conscript (like a draft) a number of units. the draft rate and total amount that could be drafted would be determined by the size of the city (or the presence of a general). and for a period of time they would train and gain strength. buildings like a war academy might help accelerate this rate (and give more early promotions). of course a city's commerce, growth, and production rate should be affected as more and more men are taken from their homes, family, and jobs.
starting the game out with no-loyalty cities across the map, to represent the un-organized peoples out there instead of an empty desolate map. kinda like the barb cities but they would not necessarily be as unfriendly and could join your civ (would act more like goody huts, but wouldnt disappear). given enough time one or more of these cities could rise up and form their own civilization.