Trials of major terrorists happen quite often in Europe, but in America, it has taken 2 decades since 9/11 for the trial of the confessed mastermind to even start in military court. (This is longer than it took from the end of the Holocaust to capture and try Eichmann).
Why is it so hard to put someone who has admitted his guilt and where there’s lots of evidence on trial?
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).
A complete analysis would be a major research project, but here is a summary: read this for more details. Jurisdiction has been a significant factor. Initially he was to be tried by a military commission (a panel of active duty officers). Defendant and co-defendants represented themselves, and were skilled in slowing the process. The presiding judge was unexpectedly replaced, and defendants indicated that they wanted to plead guilty, which raised legal questions as to whether the new presiding judge can accept a guilty plea, and also involved competency hearings for some of the defendants.
The trial was to be transferred to civilian courts under a new administration in 2009, and the military commission charges were withdrawn. There was a large political stink about holding the trial in New York, and a further complication was that the defendants' lawyers were not allowed to travel to Cuba to consult with their clients (I assume it's clear why that's a problem). Laws relating to Guantanamo Bay and using federal funds to transfer detainees from that facility were passed, so the matter was transferred back to a military commission, and in May 2012 a military trial started. The is a long set of "issues" regarding e.g. the speakers being cut off, female guards, motions to recuse, access to information that has been classified, and then finally a trial date just in time for COVID-19, but it was restarted a few days ago.
Your question is really a political one, not a legal one. After 9/11, the Bush administration, with near-unanimous support from both parties in congress, made a decision to dismantle legal rights that go back as far as the Magna Carta. The military tribunals are not real courts. In a real court, there would be a presumption of innocence, due process, and at least some doubt about the outcome. The military tribunal process was designed precisely as a way of eliminating these factors. The whole setup at Guantanamo was designed as a way to allow indefinite detention without trial.
it has taken 2 decades since 9/11 for the trial of the confessed mastermind to even start in military court.
There are two incorrect premises in this statement. One is that the military tribunals are trials, and the other is that KSM has confessed. KSM confessed under torture, and a confession under torture is no confession at all.
There is no legal answer to the question of why the government betrayed the constitution in this way. It has to be seen as a political decision that took place as part of a broader demolition of civil liberties from 2001 to the present. In addition to torture and indefinite detention without trial, this destruction of civil liberties includes all of the following: mass electronic surveillance; murder of US citizens (1, 2, 3) in retaliation for political speech; and a partially successful full-scale attack on the first amendment (1, 2). These attacks have come about with the support of both political parties and all three of presidents Bush, Obama, and Trump. Their superficial initial motivation was anger at the 9/11 attacks, but they should also be seen as part of a world-wide trend toward authoritarian populism, as in places like Poland. Some of these places, such as Poland, have never had any history of democratic institutions or the rule of law. In the US, polls show a decay in the electorate's respect for democracy. For example, the portion of the population that says it's important to them to live in a democracy has fallen from almost 3/4 in the generation that fought WW II to about 1/3 among millenials.
