"At the end of the Council of Nicaea paragraph, "The point here is this arbitrary collection of writings that left out a treasure trove of ancient writings, including the Nag Hamdi texts, skewed what Christianity became."

Indeed. That doesn't alter what Christians believe about the divine inspiration of the Councils, but certainly there are quite a few early texts which, if taken as authoritative in place of or in addition to Canon, would substantially alter Christianity.

Of course, as a Muslim, I hold the belief that Paul substantially altered the teachings of Christ, which is a position taken by quite a few unbiased non-theists.

"And at the end: "Wouldn't it preferable to fully inspect our cultural and religious upbringing and inspect the values and principles from many sources to develop our own set of values and principles instead of blindly following those that were instilled in us?""

Some theists seem to take the position that questioning one's faith-based values and principles is a demonstration of disbelief. I disagree with that position.