Speeder, plenty of the 9/11 conspirators had not been in the U.S. for years before 9/11, if at all. KSM and Ramzi bin al Shibh were caught in Pakistan, but hatched their 9/11 plot in Germany, Saudi Arabia and Afghanistan.
AFAIK, bin Laden has never been in the U.S. and began the 9/11 plot in Sudan and directed its execution from Afghanistan. Where would you suggest we prosecute them? And would you want to risk another OJ-like fiasco with such defendants, all the while watching the prosecution have to keep quiet to keep from revealing intel-gathering methods and other classified info from coming out in open court? Why should we be alerting still at-large al Qaeda folks that we have some of their cohorts in our custody, which habeus corpus hearings would surely do? Our normal "justice" system rules don't work with this stuff.