For my part, I'm a bit disappointed by the ruling, if for no other reason than that a finding of incompetence might have made Padilla the first person in U.S. history to be imprisoned under just about every possible legal theory. Recall that Padilla was: first, held as a material witness; second, moved to military custody; and third, transferred to the civilian criminal justice system. A finding of incompetence to stand trial would have resulted in psychiatric evaluation and possible treatment, but had Padilla's condition not improved, he then might have been fourth, civilly committed as mentally ill and dangerous.
Note that the legal standard of proof differs in each of these contexts, as does the nature of the detention. The fact that our legal system has been sufficiently malleable to permit Padilla to slide among them suggests that there is something seriouisly amiss, either in this case or more broadly with the legal categories. At the very least, one would have hoped that by now the government would have proffered some reason why Padilla was classified as an enemy combatant and why---other than fear of a loss in the Supreme Court---he was then reclassified as an ordinary criminal defendant.
Of course, the legal system is not done with Jose Padilla. Should he somehow be acquitted, perhaps he will then be found to have avian flu, requirng that he be quarantined.