You can change the max skill caps in Skills.txt by changing the second numerical value. Though there are hard-coded limitations for each skill.

Skill such as Ironflesh and Riding can go to 15 max while Surgery can only go to 12. I guess +8% chance is better than a poke in the doodle.

There is apparently a way to circumvent hard-coded limits, but it's pretty involved. This would likely involve knowledge of the module system.

Such changes might require a new game. Haven't tested this myself.

I'd say the simplest answer to the question is to make sure as many companions as you have use blunt not edged or pointed weapons. This does not solve what your troops equip but it at least gets more of the enemy getting hit by blunt weapons (which can knock unconscious) instead of piercing or edged weapons (which just kill when they take the enemy below 0 hit points).

Unless you have source code (in which case I would edit module_troops.py to substitute blunt weapons for some of the troops - notice manhunters and their upgrades use blunt weapons) this is about as far as you can take most mods. Also notice archers generally use pointed arrows so these will not be the troops you want to rely on for taking prisoners.