This is a fairly simple situation that was made into an impossible quagmire by the duplicity of the Bush administration.
Prisoners of war can be held for the duration without criminal charges, but they must be designated as PoWs, with all the protections provided under international law. The Bush administration did not want these protections, for reasons we are all aware of, so they created the bogus status of “enemy combatant.” This has no standing under international or common law. With our original operations in Afghanistan and Iraq having officially ended, one could argue that PoWs from those conflicts must now be either released or charged with crimes and brought promptly to trial.
Those PoWs indicted for crimes can be tried in the federal courts, or by military tribunals when permitted under international law, but the same due process would apply as in any other court. Republicans, and the RW media, persist in asserting, implicitly and sometimes explicitly, that indicted terrorists do not have the same rights as American citizens. In fact, citizenship has nothing to do with due process. Due process applies to anyone who appears before an American court.
Finally, as commander in chief Obama can release PoWs at his discretion alone. He can also decide where they are held. Congress is trying to tilt the balance of powers by attempting to interfere with this authority.