Thinking out loud about the current military system.
Problems with the current system:
Too few light cavalry. This means horse archers come too early and are too powerful at the beginning and too weak at the end.
No good distinction between light/heavy infantry. Current system is odd mix of armor and tactical role.
At any given time, vanilla civ has 7 units available: Archer (archer, longbow), horse (chariot, horse archer, knight), polearm (spear, pike), melee (sword, mace), anti-melee (ax, crossbow), siege, recon. With any more, it becomes hard to make distinctions or chose what to build. We currently have: light cavalry, heavy cavarly, archer, polearm, sword, anti-melee-melee, siege, extra (mounted inf., longbows, arquebusiers), recon. 9 is too many. "A designer knows he has achieved perfection..."
Proposed corrections:
Light cavalry will be pillagers and explorers/sentries. We will eliminate recon. Light cavalry will be weaker than just about any other unit comparable unit, but with high withdraw, extra speed, and flank attacks against siege, will still have a useful role. Western europe eschewed light cavalry during the high middle ages, so we will use mounted infantry art as a "mounted seargent" for the "light" cavalry in the west during this time and horse archer in the east/south.
Polearm is worthy of its own distinct class which will allow promotions to counter them and simplify things conceptually.
Arbalest will just upgrade to longbows, eliminating the last extra unit.
That gets us to 7.
Further cuts could come from combining the axe/sword/maceman/heavy-sword lines. This would be appropriately done like: Axe > Sword > Heavy Sword > Maceman. Eliminate all that anti-melee stuff and just make these guys stronger than polearms and with some bonus versus polearms. Then our classic RPS is:
Heavy Cavalry > Melee > Polearm
Light Cavalry, as explained, would typically fare poorly against any of these in direct combat.
Archer is a distinct class and good city defender. Melee (and possibly polearm) are the only unit categories to get city attacker, and melee would be the preference.
Armor piercing units should work only against their own era (i.e. specify targets for crossbows, longbows, axe, maceman). Alternatively, if we make the guisarmier unit a little less armored looking, then we can give an anti-heavy-cavalry and anti-melee bonus to the armor-piercing guys.
Peasant levies. We have introduced early conscription to simulate peasant levies. These units could be another class line (especially if we can we make them not-buildable?), but would have to be another class if we give anti-melee bonus. Another option is to levy from the polearm line (as it currently partly works). Conscription is not important later on in our period (re-appearing only with Napoleon), so feudal levies should become useless after gunpowder starts to show up.