Waging the legal system against our enemies won’t produce very satisfactory results, I’m afraid. If it would, we would require fighter pilots to have law degrees.
You do have a point given the rise of stateless entities for the very purpose of carrying out wars on superpowers. I think that the distinction of who is a combatant and who is just a curmudgeon is something we can handle unless you are doing the mental gymnastics of the Obama Administration by trying to deny that we are at war against radical Islam.
Please do not presume to know with whom I am at war. Islam is a cancer, a festering boil on the arse of humanity; but it is not a legitimate target for war by the United States. 5th century culture, practiced by political Islam may be. Back to my point : this exemption from the fifth amendment does not only cover militant Islam, but covers anyone they decide it covers.