In fact, OBL was listed as a co-conspirator for the terrorist attacks on 9-11:
"Specification: In that
Khalid Sheikh Mohammed, Walid Muhammad Salih Mubarak Bin'Attash, Ramzi Binalshibh, Ali Abdul Aziz Ali and Mustafa Ahmed Adam al Hawsawi, persons subject to trial by military commission as alien unlawful enemy combatants, did, at various locations, from in or about 1996 to in or about May 2003, conspire and agree with
Usama bin Laden,
Ayman al Zawahiri, Mohamed al Kahtani; Mohammed Atef(a/k/a Abu Hafs al Masri),
19 individuals who hijacked four commercial airliners on September 11,2001":
http://www.defenselink.mil/news/d20080509Mohammed.pdf
Khalid Sheihk Muhammed was indicted for 9-11 because he was not indicted for any other terrorist attacks. By the FBI's protocol he would have not been indicted for countless other terror attacks following 9-11, as it would have been redundant and a waste of time & effort.