The problem I see in Theodicy is that it takes an interesting bit of the PF, and processes it into a story that can be distilled down into one or two simplistic, moralistic elements. The most striking of these in my opinion is "Loyal, religious amarrians are stupid, weak-willed, and do lots of evil things. Once they switch sides, though, they're good, honorable men who do great things for the good of humanity."
While I was reading Theodicy, I was struck by how I saw this tenet presented again and again. By the mid-end of it, (roughly where the Amarrian Admiral returns to the Empire) I felt as if I could predict the remainder of the storyline, simply by applying this tenet and crossing it with what I knew of the Amarr-Jove war. While to some degree I suspect this is something of an inevitability, especially in a story where the end was a given, I feel that being able to completely, totally, without fail predict every little detail of the remaining plotline, the story has become to one-sided and simplistic for my tastes.