I had the same idea! 
http://discourse.stonehearth.net/t/combat-unit-skills-special-attacks-limit-breaks/22232
But I love this idea. I like the idea that a thought bubble pops up or their Heart goes gold and if you click it, the game pauses and you get to line up a special attack. This would bring more RPG elements into combat, plus make it more engaging without interfering with the AI (since’s it’s just a programmed attack).
Footmen could have Dash Attacks, a Critical Stun Attack (like you say) and a self boost that ups their Atk Spd and movement speed (to close distances to get to archers)
Knights could have a Counter attack (raised shield as you say), whirlwind or blowing on their horn for AOE aggro
Archers could have a guaranteed critical hit, a leg shot that stops movement temporarily or special arrow (fire, poison, etc) depending on what special arrow they have equipped.
Clerics could have an instant big heal with a lot of range, an AoE Blind/Stun flash, and the ability to buff players with def/atk/spd boosts depending on what special book/tome they have equipped.
I think this could really make combat much more interesting and enjoyable and make it fun from beginning to end of the game.
Thrilled to see someone else thinking exactly along the same lines! Great minds think alike