But even as more questions swirl around Benedict and his alleged role in the cover-ups of pedophile priests, John Paul's stellar reputation is suddenly taking a subtle beating.
A miracle ascribed to John Paul that is a prerequisite for his canonization has been questioned, and one of church's highest-ranking officials has said that John Paul ignored Benedict's pleas to mount a full investigation into sex abuse accusations against the archbishop of Vienna.
A Polish newspaper, Rzeczpospolita, reported that the former head of the Vatican's saint-making office, Cardinal Jose Saraiva Martins, has said that doctors may have doubts about a nun who said she had been cured of Parkinson's disease after praying to John Paul. They are investigating whether she might have had a similar condition that can go into remission. (Martins, who remains one of Benedict's top aides, also told reporters there was "a conspiracy" against the church, without specifying who was responsible.)
And in another blow to John Paul's legacy, the controversial order the Legion of Christ formally apologized last week for the behavior of its founder, the late Marcial Maciel Degollado, whom John Paul staunchly defended despite allegations of abuse dating back to the 1950s. Maciel is believed to have sexually abused young seminarians and fathered at least three children.
As doubts were being raised about the spotlessness of John Paul's 26-year reign, a Vatican spokesman on Tuesday responded forcefully to those calling for Benedict to resign, saying that they clearly did not understand how the church operates.
"This is not some multinational company where the chief executive is expected to take responsibility," Federico Lombardi told The Washington Post. "The pope is not personally directing the actions of priests around the world. He is their spiritual leader, and he is one who has acted very clearly to confront this problem."
Lombardi's statement meshed with remarks made by Cardinal Christoph Schoenborn of Vienna. On Sunday, Schoenborn told Austrian TV that Benedict, then Joseph Ratzinger and head of the Vatican office in charge of clerical sex abuse, pressed John Paul in vain to fully investigate then-Archbishop of Vienna Hans Hermann Groer, who stepped down in 1995 after being accused of sexually molesting a schoolboy.
After Groer resigned, allegations that he had also sexually abused monks surfaced.
Reuters reported that Schoenborn said other curia officials persuaded John Paul not to investigate Groer because of the bad publicity it could bring.
"The other side won," Schoenborn said. He added that Benedict is not "someone who covers things up. Having known the pope for many years, I can say that is certainly not true."
Recent reports involving the current scandals also note that John Paul seemingly rewarded Cardinal Bernard Law after he was implicated in some of the cover-ups of clerical sexual abuse in Boston when cases there exploded in 2002.
After Law's resignation, John Paul appointed him in charge of the grand Basilica St. Mary Major's in Rome, where he remains part of the Roman curia and lives in a nearby palazzo.