David Cole, writing in the New York Review of Books blog, has this essay on the President's decision not to veto the NDAA. Key passage:
the law as amended continues to contain extraordinarily dangerous principles. It creates a presumption in favor of indefinite military detention for foreign al-Qaeda suspects, even if a criminal arrest and prosecution would be the preferred course. And it imposes this presumption even for foreigners caught within the United States. While the law permits the president to waive that, the presumption is still wrong: given its inconsistency with basic principles of due process, indefinite military custody should be the last, not the first resort.
Equally problematic, the law puts Congress’s stamp on a dubious—and untested—interpretation of military detention authority. The law provides that indefinite detention without charge may be imposed on anyone who has provided “substantial support” to groups that are “associated forces” of al-Qaeda; but it leaves undefined what constitutes “substantial support” and which groups might qualify as “associated forces.” Thus far, the lower federal courts have upheld detention of al-Qaeda or Taliban members, but not mere supporters, much less supporters of associated forces. And there is much dispute about whether the laws of war permit detention in those circumstances. Now Congress has essentially predetermined that question. Unless this and future administrations construe these provisions as limited by the laws of war, they risk authorizing detention that the laws of war would not.
Most disturbingly, the law still effectively prevents President Obama from closing Guantanamo. He can’t use any funds to build or modify a facility in the United States to house Guantanamo detainees—a necessary precondition to closing the prison. He cannot transfer any Guantanamo detainee to the United States, even to face criminal trial. And he cannot release any detainee to another country without meeting onerous certification requirements regarding that country’s security measures that, until now, have proven impossible to meet. (To its credit, the administration did get the conference committee to water down the certification requirements somewhat, but it still seems unlikely that they will be met.)