Legal:

1. Evidentiary issues may make it difficult to secure convictions for all crimes alleged, whereas a military court can take into account evidence that a civilian court cannot.
2. Procedures followed can lead to major questions regarding whether or not a trial is proper, whether for failure to properly administer Miranda rights and in a timely manner or for other reasons.

Moral:

1. The cost is exhorbitant
2. It provides the defendants a forum to criticize the US and make their jihadi statements
3. It will be a media circus regardless of media access

Reid, Padilla and Moussaoui were all, unlike KSM, arrested in the United States (Reid and Padilla upon arrival). This is a vital distinction from KSM.

You spoke, in your other response, about how great the Federal court system is at making sure terrorists don't go free and also showed you are labouring under the illusion that my understanding of procedural flaws leading to acquittal is based on watching prime time television.

If Miranda rights are not important as you claim to "know from studying terrorism law" (once again, what law school did you study this at?) then WHY did the FBI start reading Miranda rights to combatants captured in Afghanistan earlier this year?

The answer is clear. Testimonial evidence obtained prior to or without a Miranda warning will be thrown out in Federal court. While we're speaking about Reid, Padilla and Moussaoui, let's go through the trials of them:

REID

Assisted the prosecution greatly with his guilty plea and behaviour in court generally. If only every case were this easy.

PADILLA

Many of the counts against him were summarily dismissed for lack of evidence and only reinstated on appeal by prosecutors. Ultimately, he received 17 years, mostly for "aiding terrorists". The case is STILL ON APPEAL due to the harshness of the sentencing for a conspiracy crime.

MOUSSAOUI

The trial was drawn out for five years due to his refusal to plead either way to the crime. The judge refused to allow the death penalty and that issue had to be appealed all the way to the Supreme Court. Moussaoui appears to have snapped at some point, however, and started doing everything he could to incriminate himself with crazy theories, thus leading to life in prison.

With the exception of Reid's trial, these trials were expensive and damaged the fabric of the US Justice System. Military tribunals would be better. The problem that the Bush Administration had was that it didn't want to give the defendants ANY Constitutional protections. I'm sure the Obama Administration could devise a fully Constitutional system of military tribunals to keep the proceedings out of the media, preserve the ability to use evidence not available in civilian trials and keep costs down.