You said:
What do you say when people question:

1. the cruelty of the Inquisition?

We answered a similar question to yours here:

• Can you explain what the Church did so wrong during the Inquisition so I can clarify this issue?

In addition, here are other web pages that will assist you in replying to this issue:

• Inquisition.
• What is the Inquisition? by Catholic Answers.
• Inquisition: Introduction from Fordham University.

2. the burning of witches and Jews?

A historical note: Such executions were done by the state, not by the Church. In many cases, they were done over the protestation of the Church.

Brian, if you are expecting members of the Catholic Church to be perfect, you will be disappointed. Sin is part of the human condition, and people will sin, even priests, bishops and popes. This does not, however, mean that the Catholic faith is not true.

I also think it is unfair to hold people, or the Church today, guilty for the sins committed by former Church members centuries ago, whether they were part of the Church hierarchy or not.

• Are you going to refuse to be an American because America endorsed slavery for a hundred years?

3. the Church's military conquests?

• Can you give me an example?

4. the lack of inclusion of women in the Church hierarchy?

The male priesthood is a doctrinal issue within the Church.

• Why?

Because Catholics believe that Christ instituted this sacrament as a sacrament of service for the faithful in the Church. When a man is ordained a priest, the Lord puts a special, permanent character on his soul. Through Holy Orders, Jesus, who is 100% man, (1 Timothy 2:5) uses the physical bodies of (priests/men), and acts through those bodies to give sacramental graces to His Church members so they can grow in holiness.

When you go to Mass and hear Father say, "This is My Body", it may sound like Father's words, but they are actually Jesus' words. He is speaking through the (priest/man), and using his body.

The same thing is true with the sacrament of Confession. You may hear Father say, "I absolve you", and it may sound like Father's words, but they are actually Jesus' words being spoken through the (priest's/men's) body.

The same is true for the other five Sacraments.

In the Pope's recent letter, he himself admitted, that he has no authority to change what Christ, Our Blessed Lord, has established. This is one of the main roles of the Pope: to safeguard and defend the teachings of Christ and ensure they don't change.

Here is a similar question that we answered:

• Do you have an explanation for my Episcopalian friend on why women cannot be ordained priests?

5. the twisted take on human sexuality?

You'll have to explain. This is obviously a large topic, but I can't answer your question unless I know what you think is twisted.

6. all the damned, perverted priests?

You will find everyone here agreeing, that bishops moving perverted priests from diocese to diocese, let alone the scandal of the seminary life that brings forth these kind of priests,
is terrible and is a huge scandal to the Catholic Church. We agree 100%! Here, we have to work on cleaning up the seminary life by:

• removing current seminary rectors and vocational directors that are not faithful to the Magisterium of the Church, and
• getting rectors and vocational directors of seminaries to be far better examples of holiness than they have been.
  
  A few good men in the mold of St. Charles Borromeo (Patron saint of cardinals, bishops, seminarians, catechists, catechumens, spiritual directors and spiritual leaders.) in each seminary would help.

Nevertheless, the Church would also say,

"We don't leave Peter because of Judas behavior."

What I mean here is that we all are human and have our human frailties; we all are tempted into sin. That includes you, me, my friends, priests, bishops, cardinals and, yes, even the Pope himself! Side note: the Pope goes to Confession weekly.

Although we are all tempted to sin, if we live a sacramental life, it will always be much easier to live according to the life of Christ, especially if supplemented by daily prayer.

Some definitions:

So the Pope is infallible, but he is not impeccable.

Although we have, over the history of the Church — from 33 A.D. to the present day — many sinners, even in high places in the Church, we can always trust that the Divine Teachings will be protected and safeguarded from falling into satan's hands. Jesus promised this in Matthew 16:13-19 and 1 Timothy 3:15.

Here is another question we answered on the infallibility of the Pope:

• What is the gift of infallibility and how does it differ from impeccability?

You said:
Logic tells me there's very little of the Divine at work in the Catholic Church — or that there's just as much of the devil and his works.

I encourage you to take a closer look.

You've quoted mainly things that happened years ago during brief periods of history.

• How does that compare with the 2,010 year history of the Church?
  
  
• Did you know that Catholicism invented:
  • the hospital?
  • the university?
    
    
• Is there no divine work in:
  • what the sisters of Mother Teresa's Order are doing
  • what missionaries are doing to improve third world societies, or
  • the people working to help the poor and mistreated?

You've listened to what the world and the media has told you. Now, I urge you to look at the Catholic side of things. I can see from your questions, that's what you are starting to do. I encourage you to go further and read the Catechism of the Catholic Church.

Another good book to read, if you are serious about studying the Catholic side of the question is:

"Triumph. The Power and the Glory of the Catholic Church" by H.W. Crocker III

You said:
It's a big, bloody, human story of pride and human failings; one of the greatest corporate endeavors of all time and it's not very pretty.

That could easily describe all of human history.

• Is there any human institution that has escaped this?
• Did anyone promise that the Catholic Church would?

The Catholic Church is, as one person put it, a hospital for sinners, not a museum for saints.

I hope you will strive to be objective and commit yourself to finding the truth, regardless of how distasteful it might be. I think you are a person who is already doing this.