In all reality, commanders are not really that difficult to deal with. you just need to pick your battles. Plowing head-on into a DS = baaaaad idea! If you wait for them and get them alone, and if need be start your rep before you are stunned, once their stun wears off, they are easy as pie. If you are in Sol, and flying a storm, you might have to think ahead a little, get your aim computer and perfs charged, then close in just enough to get the first rocket off and maybe even a blaster shot, then lead them away from other mantis where you can man handle them mono-a-mono! This same thing applies to the assassins. You need to be the one who gets the first shots in. Charge your AC and hit them with a rocket and two blasters before they can react and fire up their aim scramblers. Usually a rocket and two blaster hits = about 60-75% dead. Again, lead the assassins away so you can fight them one on one. Usually when I am fighting a commander that is of equal rank as I am I hit my AC, then perf (on Sol), then a rocket and a blaster shot, turn and run a little and hit the rep and wait for the stun (while firing), once the stun wears off, pound em.
Chas88