As we know, Attorney General Eric Holder's initial decision to try Mohammad (and his accused co-conspirators) in federal court in Manhattan was scuttled after it came under withering attack by Republicans (who wanted them tried in military tribunals). New York City Mayor Michael Bloomberg, originally in favor of the trial being held in the city also back pedaled when the costs of the trial and the security issues raised a furor particularly from Democratic leaders in the city fearing the Manhattan trial could attract another attack.
Of late there have been reports (leaks?) of Obama officials meeting with Senator Lindsay Graham, R. S.C. (himself a blistering critic of civilian court trials of the 9/11 plotters) hoping to garner his support for closing the notorious Guantanamo Bay detention facility if Obama accepts Graham's idea of holding and trying "future" suspects within a "new legal framework," (this is apparently the Faustian "grand bargain" Obama officials have been considering, but officially denied, (according to "unnamed sources"). Funny how this writer thought we had an existing "legal framework" embodied in the Constitution of the United States!
As to the military commissions' idea of trying suspects, the acting chief defense counsel, Marine Colonel Jeffrey Colwell, at the Office of Military Commissions in the Defense Department said," It would be a sad day for the rule of law if Obama decides not to proceed with a federal trial. I thought the decision where to put people on trial whether federal court or military commissions - was based on what was right, not what is politically advantageous."
What began in the now departed Bush administration, the indefinite detention of suspects swept up in war zones (Iraq, Afghanistan) or literally anywhere the CIA and it's private contractor brethren ("Blackwater", "Triple Canopy") operated in Bush's unending "war on terror" has essentially continued under the Obama administration. Obama's talking kinder and gentler while dropping the odious "war on terror" moniker are P.R. sleights' of hand deceptions, particularly when the policies of his predecessor remain largely intact. Obama has made the whole issue of indefinite detention and trying suspects more complicated by finessing its closing of Guantanamo and failing to adhere to Holder's plan to try Mohammad in the city where the primary 9/11 attack occurred.
Obama and his administration seem to have initial conviction (closing Guantanamo within one year) but bow to political pressure when critics condemn the original decision. The same goes for Holder's initial decision on a civilian, federal trial of Mohammad in New York City.
 "Military may get 9/11 suspects' trial, White house poised to challenge plan to try them in civilian New York court", Anne E. Kornblut and Peter Finn, The Washington Post March 5, 2010.