I don't have the energy to deal with these systematically, so I will just address these points in no particular order:
1) Telescoping History
This is a common problem with people who talk about history in general, and early church history specifically. A prime example is the discussion about the influence of Constantine on the Church. Constantine's influence is far reaching, and certainly deserves to be discussed in a book on early Christian doctrine and lifestyle, however, Constantine's Edict of Milan was in 313 AD. From our 21st Century vantage point this may seem like a short jump from the lifetime of the Apostle's and Church Fathers, yet we must remember that the U.S. Declaration of Independence is closer to us in history than Jesus' crucifixion was to Constantine's Edict; Irenaeus' argument for a canonical fourfold gospel is removed from the influence of Constantine's conversion by a period of time equivalent to our own removal from the Civil War. In short, there is a common confusion about the timeline of ancient history, and a subsequent muddying in people's minds about which events have an impact on which other events.
Pagels certainly makes this mistake, arguing about Constantine's effect on the early church in a way that reveals she simply is unaware that what was going on in the 1st, 2nd, and 3rd Centuries could not have been influenced by what was going on in the 4th Century.
2) Confusing Literary Genres
The Gospel of Thomas is simply not a gospel. There is an attempt made by Pagels to compare and contrast the Thomas writings with the Gospel of John. But Thomas simply has no 'good news' to it. It is only a collection of sayings attributed to Jesus. The very attempt to label the Gospel of Thomas a gospel reveals how derivative a work it is. But none of this is addressed by Pagels.
3) Fails to Address the Historical Question
Pagels' book makes much of her recreation of the history of the 2nd, 3rd, and 4th Centuries. She paints a very particular picture of the life of the church, and of individuals within the church. And yet, the glaring omission from the book is her failure to ever address questions of the 1st Century. Not only does she not address the life and events of Jesus and the Apostles, but she never even tells us why she doesn't discuss them. In a book that takes sides on the 2nd Century debate about 1st Century history, that she herself never even touches the question of 1st Century history is a bit confusing.