Head punch: likely counters- Head punch, body punch, takedown, low kick
unlikely counters- Clinch(you move your protecting hands away from your head)
Body punch: likely counters- clinch attempt, head punch, body punch, elbows, knees for taller fighters
unlikely counters-any kick, takedowns. Usually throwing body punches requires them to close the distance, when that distance is taken away kicks become awkward. Since they drop their hand to throw the body punch, it also makes it easier to get underhooks to stop takedowns.
Punch combos likely counters-- takedowns! head punch, clinch,
unlikely counters-- kicks, if you sacrifice your mobility to throw a kick mid comb your probably going to get swarmed
Head kick likely counters-- head punch, any kick while they are recovering
unlikely counter-- body punch, takedown, clinch
Body kick likely counter-- takedown, low kick
unlikely counter-- any punch, clinch
Leg kick likely counter-- head punch, check/low kick, takedown
unlikely counter-- body punch, clinch,
Clinch attempt likely counter-- head punch, body punch, takedown
unlikely counter kicks
Takedown attempt likely counter- takedown, clinch, any punch, knee, submission attempt (higher% chance if your guy is set to give up the takedown anyway?)
unlikely counter any kick
Kicks tend to suck as counters because they require space and require you to cover distance in order to generate power. The best way to stop someone from kicking is to force them to step back. Low kicks however have some very good situations where they are useful as counters when your opponent has thrown themselves off balance. They also require much less space to generate power.
I'm not sure if the following is done in the system, but kicks are great to shut down your opponents mobility and head movement. If they have lateral movement, it is a lot easier to box/cut off the ring by throwing kicks as opposed to throwing hooks because they have a greater distance. A low kick that lands or is checked forces your opponent to stop moving, making him a target for punches. If your opponent is using head movement to avoid punches, he can easily duck into a kick or knee.
Kicks are good to break down a someone in a defensive posture looking to counter, they are horrible to use if you are trying to counter. Most headkicks that miss are usually taken on the arms, or the opponent moves back out of the way leaving themselves in a poor position to counter.