A general idea, just thought of this: Split Units up into 50's, 100's, 500, and then 1,000's. Guesstimate the size of a nation's military population (I think something like 2-10% of the general population is a good idea), and then divide by 10. The number you get will probably be roughly the size of a standing army (peace time?). A 1 Million population using these numbers has a total military pop around 20,000, and can field an actual standing army close to 2,000 strong.
Figure that Infantry will make up the bulk of the army. Cheaper than all-horsemen, less training needed than bowmen. Let's say 1,200 Inf. We could subdivide that into 12 Centuries (12 100-strong units). If we feel really snazzy we can further subdivide them into Heavy Infantry, Light Infantry, or Spear Infantry. For now let's not.
Bowmen will be important to an army, so we can expect at least a decent amount of them. Say, 500? Lot of archers. Split them into 5 Centuries, or 10 Cohorts (50-strong for our purposes). For an Ancient Warfare Simulator that's all you need (although a later setting would need to differentiate between bows and crossbows).
Horsemen and Chariots. Both immensely powerful units. About 100 each. Nobles ride chariots with their personal bowmen, while some sort of equestrian class rides horseback. Both can make a Charge, and both can support an archer, although the chariot can do both at once.
And 100 left over for special units. Berserkers, war-dogs, war-pigs (burn baby burn!), Artillery, Assassins, etc, etc.
Give each Unit 3 Stats: Tech, Training, Morale. For Tech, Bronze armor and weapons nets +1, anything less is 0 or lower. Iron equals +2, Steel is +3, and so on and so forth. This modifies offense and defensive rolls. Training works similarly,+0 representing raw recruits and +4 representing Elites. Add this to Attack or Defense, but it takes a Full Round to switch. Morale works like a Will Save. This number is equal to the Charisma Modifier of the leader of the Army, or if they are led by a character with a higher Charisma use that. Every time an attack connects with a Unit (or their own attack failed to connect), it costs a number of casualties equal to the difference between the Attacker and Defender rolls. Roll a Morale Save 1d20+casualties, or lose a point of Morale. Some attacks cause extra Morale Loss (fire attacks, attack in the flank, etc). When a Unit fails a Save while at 0 Morale, they run if able.
Set up the two armies, decide who attacks first, and start rolling. Most Units should be the same on a side. Add a small modifier depending on who fights who. Archers get +1 against Cavalry, Cavalry gets a +2 against Infantry (except Spearmen) and Infantry gains a bonus against archers. Add modifiers for tactics like flanking or suppression fire, or making lanes when the scythed chariots attack.
Roll until one army remains.