It's a terrible decision to prosecute Khalid Sheikh Mohammed like a common criminal. We will be handing intelligence over to our enemies. During the trial of the 1993 World Trade Center bombers, intelligence that we were interested in Osama bin Laden was communicated from "secret" discovery documents to OBL's ears within two weeks. We will be handing KSM a public forum from which to put U.S. foreign policy on trial - a factor that some believe may actually underlie the reason for the transfer, as it gives the Obama Administration the ability to try Bush Administration officials without actually bringing them to court. On the plus side, if KSM behaves true to form, it will be for anyone to continue to deny the explicit destroy-America message his brand of radical Islam preaches (but does anyone seriously deny this now? who that still needs convincing will be convinced?).
One reason for disapproving of the trial that I've heard but disagree with is that it sets perverse incentives, i.e. if you kill our soldiers abroad, you are tried in a military tribunal, but if you kill our civilians at home, you get the enhanced protections of a civilian criminal trial. I highly doubt terrorists respond much to such incentives. Consider the already severe disincentive of committing suicide to carry out your attack, for example. If you're willing to do that, I don't think the moderate difference between the civilian and military courts is likely to change your behavior.
But worst of all, it's effectively a show trial. Attorney General Eric Holder has already guaranteed a conviction, and President Obama has essentially guaranteed an execution. These guarantees are not possible under the rule of law. If KSM is not convicted, will he be released? Of course not: that would be political suicide. I wonder if Obama is playing a subtle game here: suppose KSM were found innocent on the technicalities of his not being Mirandized, the waterboarding, the interrogations, the "illegal" (they will say) detainment at Guantanamo, etc. Then of course he would be re-arrested on some other charge, but now Obama could blame the Bush Administration indefinitely. "Well, we tried to legimitize his arrest, but because of all the mistakes they made, we can't. Don't blame us!" Considering that Obama is still blaming Bush for everything he can ten months after his inauguration, the strategy seems possible.