I had a reader submit a question about responding to the "Letter to a CES Director". He wanted a response. FAIR Mormon has done a great and thorough response which you can find here. But I want to talk about things that matter, and not just the multitude of details which tend to lose sight of important issues.
The Church did engage in covering up perceived weaknesses of leaders in the past. Typically these efforts were led by people and sometimes leaders who feared for the impact of certain issues on members' faith, or on public perception of issues.
No one should lose faith because past members or leaders lacked faith in the ability of members or non-members to fairly process the issues involved. It is however easily demonstrable that current leadership does not feel that way. The Joseph Smith's Papers project sits front and center as the most thorough and transparent publishing effort around an historical figure ever. You don't do that if you are afraid of what will be discovered.
But there are a lot of issues, and I will only discuss a few. First, most leaders were ignorant of indepth historical matters. Thus you get a statement from Harold B. Lee that based on information from Joseph Fielding Smith that Joseph Smith never did ordain any black men. With the documents we now know exist, such a position is simply not true. But ask where Joseph Fielding Smith got his info? Well, at some point the first Presidency in the early 1900's reaffirmed the Brigham Young ban on ordinations, which Brigham Young attributed to Joseph Smith.
So did JFS look at every document? Probably not. Even as the Church Historian, he had little time and no training to go through the Church's records. It was enough that he knew that his father had endorsed the ban. And in the 1960's, the Church did not have resources or inclination to challenge Brigham Young's ban which had been reaffirmed by nearly all Church presidents down to that time, unless they received a revelation.
If the Church leaders could only sit for a year or so and get a crash course on LDS history from original documents and eyewitness statements, and then get deeply versed historians to walk them through it, then we could claim that General Authorities are also well informed historians. But that is not now nor has it ever been their roles.
But there is a second point, much more important to consider. That is, not all evidence is of equal value. So understand this point clearly. Someone may want to say the evidence for the Book of Abraham or Book of Mormon geography, or First Vision documents is weak. I personally am fine with it, but let's pretend you are critical of those topics. Those are truly secondary. Primary evidence is physical and spiritual about the Book of Mormon.
I have written extensively on the physical evidence and witnesses of the Book of Mormon. As a whole it is excellent. In detail, it is amazing. Try as critics like Jeremy do to attack the reality of the Book of Mormon, their arguments inevitably lead to accounts from secondary or tertiary sources because the primary sources are consistent and supportive of each other. There can be no doubt the Eight Witnesses saw and handled something. In 1827, when Joseph brought the plates home for the first time, more than a dozen folks handled the plates, though they did not see them. At least several of them would later become witnesses. It requires one to believe JS had in a finished form the plates in 1827, at a time when he was newlywed and flat broke, because they could feel the engravings, handle the spine, etc. Keep asking the question: How could he do that?
I once heard Dan Peterson say the purpose of the plates was to be a thumb in the eye of the critics. You must, if you choose to lose your faith, explain how Joseph Smith could have put the plates together without anyone being aware of it; having the skills to forge and punch and craft them into their shapes; to paint them in a way that the primitive paints of the early 19th century would be unnoticeable to close scrutiny; and to convince people who in many cases left the Church and were offered significant fortunes to tell the "truth" about the plates. In all these things they fail. The current attempt to discredit the witnesses by saying the plates were immaterial and only viewed spiritually requires one to twist what the witnesses actually said.
Secondly, there is the spiritual witness. The Bible is replete with statements that God is received and perceived spiritually. There is no way to come to a knowledge of truth by study alone. When I discuss the problems with leadership, the Bible, the Book of Abraham or other issues, there is no intent to make people think these are not trustworthy. I usually discuss such things due to the double standards imposed by critics. My personal problem with the critics usually comes down to two issues: Their hypocrisy in what they consider evidence, and their lack of effort in finding balanced evidence. When you hear Richard Bushman discuss Joseph Smith, he discusses every aspect of him, good and bad. The critics will only discuss the bad, and only occasionally throw a bone at acknowledging there was some good.
People may rightly say there are things which could cause one to think twice about the Church. But such conversations miss the only point where God has said in the scriptures he will provide proof to the faithful: A witness of the Book of Mormon.
My personal experience, which I have outlined elsewhere, goes beyond this. But it started here.