Some feared a high-profile terrorism trial would put the city at risk. Others said a civilian courthouse, with all the rights afforded defendants there, was no place for a terrorist.
Obama, who came into office promising to close Guantanamo Bay and prosecute terrorists in federal courts, buckled under the pressure and pulled the case back to Guantanamo.
Since then, not much has changed at the naval base in Cuba. Mohammed is one of 164 men held there and one of six facing trial. Those trials have stalled largely because of legal challenges to the commission system itself.
In federal courts, however, the Obama administration is quietly churning through terror cases and putting many terrorists away for life.
One of the first key cases was against Ahmed Ghailani, a former Guantanamo detainee who was transferred to New York during the Bush administration. He was convicted in 2010 and is serving a life sentence in prison.
Last year, Mohanad Shareef Hammadi, an Iraqi man, pleaded guilty to terrorism charges in Kentucky and was sentenced to life in prison without parole. Hammadi's co-defendant got a 40-year sentence for his role in a plot to ship weapons and cash to insurgents in Iraq.
Ahmed Abdulkadir Warsame, a Somali citizen accused of helping support and train al-Qaida-linked militants, pleaded guilty earlier this year. Like al-Libi, he was questioned aboard a U.S. warship before being turned over to the civilian justice system.
Each new trial brought fresh criticism from Republicans, but that criticism diminished each time.
Some Republican lawmakers criticized Monday's announcement that al-Libi would face trial in court. They questioned whether interrogators questioned him long enough.
"It certainly begs the question whether rushing foreign terrorists into U.S. courts is a strategy that is in the best interests of the United States," said Rep. Bob Goodlatte, R-Va., the chairman of the House Judiciary Committee.