Here's a problem: They are being put on trial as if criminals for an act of war. To Mohammed and his cohorts, this was not just a bomb-and-arson. This was an act designed to cripple the United States with fear. It was a strike at financial, defense and (probably flight 93's destination) political centers. We are not involved in a police action with these Islamic extremist terrorists. We are involved in war. And that creates different parameters.
Here's another problem: This will be profoundly disruptive to the City of New York. Security will have to be ridiculously tight. It will cost money to guard these guys, and prevent attempts to kill them by both their colleagues and angry Americans. And for those directly affected by 9/11: I don't think having these guys around, and hearing all the details of the trial will exactly help everyone's psychological health.
A third problem: Appeals and technicalities. We all know about trials where the perp's guilt was obvious and proven, but the bad guy was released due to some "technicality" like a problem with evidence or interview. Did these guys get read their Miranda rights? No, I believe they were abused some, and their families threatened. Hmmm, that sounds like it could be a problem.
The current administration is so busy apologizing for America and trying to appear non-threatening to the world that we are endangering ourselves by underselling the determination of Islam extremists to wage war against us. This is war, not a police action. Thus, those who violate the rules of war should be tried in the military milieu, not civilian court. This is a bad idea.