Maybe skirms could be made more viable counter for conqs making them represent cavalry archer class. It would increase skirms attack by 2 against conqs. Also removing their melee armor wouldn't change things too much. If melee units would be too strong against conqs then, problem wouldn't be in the unit anymore more like in the controller of it.
Exactly. Nerfing Conq melee armour does nothing to affect early or mid castle play. Make Skirms a stronger counter and problem solved. You don't directly nerf the Spanish in any way but all the civs can now effectively counter them.
Nerfing anything but the armour on Conqs will unbalance the unit. Nerfing armour doesn't do much unless it's the pierce armour. Giving them a Cav Archer armour class would probably work better than touching their pierce armour.