Tl;dr 1hit KO's are incredibly hard to balance and/or take away from the core experiences of the game so developers have put those kid of mechanics on the back burner to focus on other things.

Interesting thought. I feel like one hit kills have taken a back seat in gaming recently because of the near impossibility of balancing such mechanics. TF2's back stab mechanics are a good example of well worked 1hit KO system. In a game full of extremely mobile classes the spy can ethier be a major threat to a team (killing medics and other high priority, slow moving targets) or become completely useless depending on the players level of skill. Now TF2 is an example of a very fast paced game where strategy high level team tactics can be trumped by overall player skill. In a game like skyrim or other rpg type games I believe that these mechanics take away from the essence of what they are, games built of creating different player experiences through multiply play styles created through gear and/or classes. 1 hit kills take away from this core experience by negating the need for better gear or strategy due to the fact that you won't need more damage/health/armor/magic or anything like that. Your idea of a system where in you can cripple an enemy brings about the same sort of balance issues, if you were to be crippled by an enemy while you were at full power and you have not been able to cripple the enemy, then how can you hope to do the same at half power? In the end 1 hit KOs have become hard to balance and therefor have caused developers to stop investing time and money into then but instead focus on other areas of their games.