Regarding Padilla. The question, to my mind, is largely simple. Is Padilla a citizen? Unless he has renounced that citizenship, he may not be deprived of it. Perez v. Brownell, 356 U.S. 44 (Warren, C.J., dissenting). If he is, he should be prosecuted for treason per U.S. Const., Art. III §3 and 18 USC §2381. As Justice Scalia explained, dissenting n Hamdi:

Where the Government accuses a citizen of waging war against it, our constitutional tradition has been to prosecute him in federal court for treason or some other crime. Where the exigencies of war prevent that, the Constitution’s Suspension Clause, Art. I, §9, cl. 2, allows Congress to relax the usual protections temporarily. Absent suspension, however, the Executive’s assertion of military exigency has not been thought sufficient to permit detention without charge. No one contends that the congressional Authorization for Use of Military Force, on which the Government relies to justify its actions here, is an implementation of the Suspension Clause.

The Court's opinion today does not question that Padilla is a citizen:

The exceedingly important question before us is whether the President of the United States possesses the authority to detain militarily a citizen of this country who is closely associated with al Qaeda, an entity with which the United States is at war;

It not being contested that Padilla is a citizen, on what grounds is he unentitled to file a habeas petition? On what grounds is he denied the rights guaranteed to a U.S. citizen? On what basis can an act of Congress supercede the requirements and strictures of the Constitution? The court does not say.

I would affirm the ruling of the district court in this case, and by the same logic, I would overrule Hamdi. I respectfully dissent.

Hamdan looks like tough sledding from a cert perspective because the military has not had a chance to conduct a "trial". With new rules, in particular, it is not so clear as it might be that Hamdan et al will be denied some semblasnce of due process.