First off, I’d say to recognize the fact that the child abuse done by priests is monstrous and terrible, and the offenders should be punished to the full extent of the law, and the victims cared for and with deep sympathy. You can’t sugar coat it. It happened, and it should be, and certainly has been addressed by the Catholic Church.
Second, I’d also point out that a saint is not omniscient. Some saints are given some gifts, other saints are given other gifts. Just because Pope John Paul II is a saint doesn’t mean he knew the truth about either individual cases or the scale of the problem itself.
Third, the vast majority of these cases occurred during the 60s/70s/80s, and the scale of the problem was the kind of thing that was unprecedented for its time. There are two aspects to be considered on this point. First, its unprecedented nature. Prior to this, you may have had rare and isolated cases, and often when reports of such behaviour came in, it was found to be a false accusation in order to defame the priest. At the time that this occurred, there were Communist agents actively working throughout the world to wound or destroy the Catholic Church, as it was a major opponent of Communism, and was itself actively working to end the reign of Communism in Russia. These large number of abuse accusations may have been misinterpreted to be acts of defamatory sabotage.
The second point to consider is the time period that this occurred in. It was during the years immediately following the “Sexual Revolution.” At the time, there were many cases of child abuse across many professions. The prevailing expert opinion was that the abuse was tied to the relationship developed with the particular child/youth, and that by removing the offender from the particular situation, and having them attend therapy sessions, the problem would be resolved. So, it was often the case that, for example, an offending teacher would be moved to a different school, attend therapy, and it was believed the issue was resolved. However, as it is now known, the offense repeated itself in the new environment. Catholic Bishops were acting upon the prevailing expert opinion of the time and doing what everyone else was doing: removing the offending priest from the particular parish and placing them in a different one, with the understanding that therapy would and a new environment would make the problem go away.
It wasn’t so much a “cover-up” as a combination of things. First, incredulity that most of the cases were even true. Second, the socio-political environment of the time. Third, the prevailing expert opinion of the time regarding pedophilia.
The implication that the Pope “knew” about the nature and scale of the child abuse scandal and that he deliberately “covered it up” is neither true nor supported by any actual facts. It’s speculation, plain and simple, and it’s speculation that ignores a lot of actual documented facts that imply quite the opposite.