An answer by @user6726 accurately points out some matters specific to this case, a "tree level" view, so to speak.
At a "forest level", the military commissions system that was first used had to be established from scratch leaving myriad issues of first impression and constitutional validity issues unresolved, unlike ordinary civil courts where these matters are already settled law. Many of these issues were difficult ones because the system was intentionally stacked against the defendants. This was an unexpected result from the perspective of the people who enacted the statutes authorizing military commissions trials, who expected them to be more swift and to be less favorable forums for defendants. But they failed to recognize that all judicial and quasi-judicial proceedings conducted by the U.S. government, even military tribunals, are subject to judicial review under modern U.S. law.
Failure to recognize this issue is one of the main reasons that the military commission system produced so few results, while terrorism prosecutions under criminal laws in the ordinary federal trial courts were conducted with minimal difficulty relative to ordinary criminal prosecutions. It also failed to recognize that unlike typical civilian criminal defendants, terrorism suspects are often happy to plea guilty and claim credit for actions that these defendants viewed as heroic and justified.
A key substantive issue in this particular prosecution is that important evidence against him was either obtained through torture, or was "fruit of the poisonous tree" evidence obtainable only as a result of information obtained through torture, in a manner that would not be admissible in civilian criminal proceedings.
Another key mixed procedural and substantive issue was a military commission policy that treated much of the relevant evidence as classified secrets for purposes of national security, which impacts which personnel could be involved and created procedural questions not presented in ordinary courts. The U.S. government could have declassified the relevant information, but chose as a matter of policy to conduct proceedings while the information was still kept as a national security secret (in part, because the U.S. involvement in torture and the low level authority of most of the other military commission defendants was embarrassing to the U.S. government).