I usually determine two groups for AP Infantry: Light and Heavy
I prefer using light AP equipped troops for flanking forces since the more amoured guys hold the line while the less armoured AP units (like Eastern Axemen, Drapanai, Agrianikoi Pelekephoroi and other "Light armour breakers") race behind the enemy infantry, throw there Javelins and charge from behind - There ideal for this task because there weapon gives them a chance against better defended soldiers (most of the armoured enemy won't even notice what cut them apart from behind), but there lack of own armour means they would have trouble fighting head on.
"Heavy armour breakers" (I thinkKomatai Epilektoi, Thraikioi Rhomphaiaphoroi, Loricati Scutari fall under this category) are able to fight head on against armoured troops, although they themselfs are also somewhat vurneable to AP weapons. The ideal case would be to use them to ambush elite forces instead of wasting them to attack large numbered and unarmoured units.
I also think the ideal tactic against "light armour breakers" would be to rain arrows on them or attack them with large unarmoured units (the enemy will cause large casualities unless weakend by skirmishers, still it is more worth it then to send vauleable amoured soldiers against them).
Against "Heavy armour breakers": rain them with missile weapons (prefereably AP) and try to surround them (attack with light mass units first, later with heavier ones).
Cavalry charges are a good way to decrease the number of AP units: "light" ones may be more numerous, but the lack amour to defend them against repeated charges - they get cut down to size step by step. "heavy" ones are better defended, but there low numbers means that charges can take down a larger prozent of them. (in both cases it is advised to pull back the cavalry after every charge - in melee AP troopers can cause unnecessary loses to the horsemen, always try to mass charge them (3-5 cavalry units at once) so the enemy infantry might even rout after impact.
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