Among the issues was the widespread practice of encouraging divorced and civilly remarried Catholics to receive the Eucharist, despite the Church's clear teaching that these relationships were objectively irregular and the practice itself was a witness contrary to indissolubility of marriage.
Ratzinger also noted "repeated instances" of allowing non-Catholics to receive the Eucharist at Mass, and instances in which Catholics were allowed to receive communion at Protestant services.
In total, five areas needing attention were outlined. The others included concerns that some local Catholic hospitals were providing contraceptive sterilization services, that Church teaching on homosexuality was being distorted or obscured through the influence of outside groups, and that there were problems with priestly formation of seminarians.
While the CDF recognized that Hunthausen had made positive efforts to respond to the criticisms, Donald Wuerl was appointed an auxiliary bishop in the archdiocese in 1986, with special responsibility for the five problem areas. Despite public hostility to Wuerl by some in the archdiocese, he and Hunthausen forged an enduring personal friendship before Wuerl was relieved of his responsibility in 1987, and appointed Bishop of Pittsburgh in 1988.
Nevertheless, an air of resentment toward perceived Vatican interference overshadowed the rest of Hunthausen's tenure. Bishop Thomas Murphy was appointed archbishop coadjutor in 1987, and Pope St. John Paul II accepted Hunthausen's resignation in 1991. Aged only 70, this was five full years before Hunthausen would have reached the ordinary retirement age for a bishop.
In 2002, at the height of the sexual abuse crisis, it emerged that police had informed him in 1986 about an investigation into the Bishop of Spokane, Lawrence Welsh in 1986. Police met with Hunthausen following an accusation that Welsh had attempted to strangle a male-prostitute during an encounter in Chicago that year. While Welsh admitted to the encounter, no further action was taken and he was allowed to continue in episcopal ministry.
In retirement, Hunthausen returned to Montana, living with his brother, also a priest. His reputation as an outspoken advocate for peace remained intact, though his time in Seattle remained a source of controversy.
While perhaps inextricably linked to controversy, Archbishop Hunthausen will be fondly remembered by many in the Church, especially in Montana and Seattle. Even many of those most often considered to be his critics considered him to be a man sincere in his convictions who, in the words of Cardinal Ratzinger, "strove with heart and mind to be a good bishop of the Church, eager to implement the renewal called for in the decrees of the Vatican Council II."