In his reply to Jack, Raha Wala of Human Rights Watch concludes: "I think the big question is why, as a matter of policy, the government continues to insist on using untested military commissions for international terrorism cases when Article III courts have proven more than capable of handling these same kinds of cases for well over a decade." I think the answer to this question differs depending on whether Raha means the executive branch when he says "the government" or whether he means the Congress. At least if he means the former, the answer is pretty simple: The executive branch insists on using military commissions because Congress won't let it use Article III courts.
Human rights activists often talk as though the use of military commissions represents a betrayal on Obama's part. But even from their point of view of someone who hates military commissions, Obama's behavior should be only part betrayal. Yes, Obama sought the MCA 2009, and his administration brought one case in the revamped commissions on its own initiative. But it was Obama's intention to move the bulk of the Guantanamo detainees slated for trial to New York for civilian prosecution--just as human rights activists wanted. And it was Congress, not Obama, that prevented that.
At this point, complaining that "the government continues to insist on using untested military commissions" instead of Article III courts risks imputing to Obama policy he actively opposed and which was imposed upon him in order to limit his flexibility. One part of the "the government"--the executive branch--does not insist on military commissions as a general proposition. In fact, it would rather try many more cases in federal court and has only very grudgingly complied with Congress's mandate. It is prosecuting people in military commissions because that is the one venue lawfully available to it. Another part of the "the government"--the Congress--does insist on the use of military commissions, but that is not the part of "the government" to which Raha's complaint is normally directed.
Raha's use of the vague term "the government" here is certainly not wrong. It is, however, imprecise. And its imprecision elides an important difference between the policy objectives of the executive and legislative branches with respect to this issue. The executive branch's position--properly understood--has been that it wants military commissions to be available but almost never to have to use them, and that their use should be limited in any event to the legacy problem of Guantanamo Bay. Much of the legislative branch, by contrast, wants military commissions to be the principal mechanism for trying terrorists, prospectively as well as retrospectively--and the legislature institutionally has insisted that they be the exclusive means of prosecuting detainees at Guantanamo. The result is a "government" policy that is something of a compromise: Military commissions are notionally available prospectively, as well as retrospectively, but decidedly not the principal means of trying terrorists in general (the executive's preference)--except at Guantanamo, where they are the exclusive means (the legislature's preference).