Catholics were no longer expected, as some put it, to simply "pay, pray and obey," but now could make their own decisions about their faith.
Another reform hallmark of Vatican II: Use of the English-language Mass.
The Vatican has now directed American churches to institute a new mass featuring an English translation more faithful to the original Latin - a mass critics say is harder to understand, less English-speaker friendly.
But perhaps the most striking example of the Vatican's apparent about-face on reforms may center on American nuns.
"Sisters, actually - ironically - really took Vatican II seriously," said Sister Mary Ann Hinsdale. "Perhaps more than other segments of the church, and that is causing some friction. We're doing exactly in a sense what the document on religious life asked us to do."
Sister Mary Ann is a member of the order of the Sisters Servants of the Immaculate Heart of Mary. She's also a professor of theology at Boston College.
"I think there's always a tendency - particularly when it comes from the Roman Curia, who in fact are the kind of bureaucracy of the church - to think they are the church and they're in control," she said.
And not long ago, the church in Rome exercised that control - launching what's called an apostolic visitation, a process shrouded in mystery allowing it to investigate orders of nuns here in the United States.
We asked Phoenix' Bishop Olmstead just why the probe was ordered.
"I think they felt the apostolic visitation of the religious sisters in our country was prompted primarily by a concern about the decline of the number of religious that we have in our country," he said. "It's really on a steep decline. And that's a grave concern."
We reached out to many orders of nuns across the country hoping to get their viewpoints about all of this.
In most cases someone would agree to be interviewed. But when the interview was imminent we would be called and it would be canceled.
In the end, Sister Mary Ann Hinsdale agreed to speak with us - partly, she said, out of concern that if she didn't, no one would.
"Do you think this apostolic visitation is something that nuns like yourself, who are out there in the world, should be worried about?" asked Petersen.
"I really don't know," she replied. "But I think the most problematic aspect of it is that we are not going to see a report, and we don't know what is going to be done with this. We were never told what was going to be done with this. And while we think this is, you know, a travesty, really, and insulting even about who we are in the church, because we think we're trying to be loyal to the church. We're trying to make, you know, plausible explanations where people are saying, 'Well, why is the church doing this? Why are they excommunicating people who are, you know, seem to be wanting good for the church?'"
"Why the nuns?" asked theologian Gary Macy. "This is my suspicion: They can.
"I's interesting that they would take the women's religious order, and not the men's religious orders," Macy said. "Although, you know, for so many centuries and centuries and centuries in Christianity, women have taken a hit first."
Phoenix' Bishop Olmsted admits he sees no future role for women in the priesthood.
Still, he says they're valued members of the church.
"We wouldn't have all our Catholic hospitals if it wasn't for Catholic sisters," Bishop Olmstead said. "We wouldn't have a lot of our Catholic universities if it wasn't for them."
It's a battle between Catholic and Catholic ... between past, present and future.
Yet, even with these differences, some things endure ...
When asked why she stays with the Church, Sister Mary Ann Hinsdale said, "Because it's my church. I have a responsibility to speak the truth that's been given to me.
"There's a lot of pain and suffering, I think, in belonging to the Catholic Church today. But I think I'm following as best I can what I think God is asking me to do today in this church as we have it."
As we mentioned earlier, Sister Margaret Mary McBride in Phoenix has consistently declined to discuss the events at St. Joseph's Hospital.
But not long ago, she did speak out at an event sponsored by an organization that often challenges Catholic hierarchy:
"As we move forward in this very disappointing time in our church, I think it's the time when we need to be the example of mercy and forgiveness and love," she said.
In fact, her excommunication has now been lifted. But, Bishop Olmsted also asked that she resign from the hospital's ethics committee. She has.
As for the hospital: To regain its "Catholic" status, the bishop insists that it must say the medical procedure that resulted in the abortion and saved the mother of four was in violation of religious and ethical policies, and will never happen again.
So far, the hospital has refused to do so.
It still cannot call itself Catholic.