Laura Olson, senior counsel for a think tank called the Constitution Project, said that military commissions -- despite reforms from Congress -- still do not afford defendants proper protections and have failed to produce convictions.
"In eight years we are on our third set of military commission's structure and only three people have been convicted," she said.
Olson advocates the use of federal courts for all those charged. "Since 2001 the federal courts have tried over 145 terrorism suspects. The system does not hinder convictions and the federal courts guarantee the protection of defendant's rights."
But in his May speech the president said he wanted to work with Congress to bring the commissions "in line with the rule of law."
Obama said, "The rule will no longer permit us to use as evidence statements that have been obtained using cruel, inhuman, or degrading interrogation methods. We will no longer place the burden to prove that hearsay is unreliable on the opponent of the hearsay. And we will give detainees greater latitude in selecting their own counsel, and more protections if they refuse to testify."
In congressional testimony last summer David Kris, assistant attorney general for national security, said that the administration will avoid "abstract bright line rules" regarding which forum for prosecution will be used. He said the administration will rely on federal courts and military commissions, "both effective, both legitimate" and that professionals will make the choice for each case "using flexible criteria established by policy-makers."
Earlier in the summer the Obama administration transferred Ahmed Khalfan Ghailani, to the United States to be tried for his involvement in the 1998 bombings of U.S. embassies in Kenya and Tanzania. Other terrorists such as Ramzi Yousef, a planner of the 1993 World Trade Center bombing and the so-called 20th hijacker, Zacarias Moussaoui, have been convicted in federal court.
Some detainees at Guantanamo are not destined for trial in a U.S. court, but instead will be handed over to other countries.
In testimony this summer, Jeh Johnson, general counsel of the Department of Defense, said that the number of other detainees approved to be transferred to another country is "substantially north of 50." Already the administration has been furiously trying to find a third country for a handful of ethnic Muslims from China -- called the Uighurs, who the administration no longer believes are a threat. But finding countries willing to take former detainees have proved a prickly subject.
"Even for those who don't seem to pose much threat, it's very difficult to get other countries to open their doors, especially when our own government won't let any detainees into the United States," said Matthew Waxman of Columbia Law School, who served as deputy assistant secretary of defense for detainee affairs in the Bush administration.
He adds, "There are also many detainees from Yemen whom we believe are dangerous but we'd like to transfer. For them, the issue is we lack confidence that the government of Yemen can deal with them adequately, and no other country is willing to take them. "
Perhaps the thorniest question of all is what to do with detainees who cannot be prosecuted yet the administration intends to continue to detain.