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His vision for Eisenhorn and the direction of the story would change completely. It's basically if you took Eisenhorn, and instead of Dan Abnett writing all of the books, you throw ADB halfway in the middle. You start going straight, things look promising, and then immediately take a sharp left turn. The recent Star Wars movies, for example, show just how if you take one director who has a vision he wants to create, then halfway throw in another director with a different vision, it creates inconsistency and confusion in the story you are trying to tell. Everyone interprets the Emperor's actions in their own way, which only goes to add more confusion to his character. There's no linear direction to who the Emperor is, what he wants, his actions, etc.
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He has multiple writers, each interpreting him in their own way. The fact that it's so large with so many books, each written by different authors, creates a level of ambiguity and confusion that is probably even greater than the Imperium itself.
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But the initial problem is the Horus Heresy, in terms of 40k, should have remained a time of legend, when the Emperor walked amongst mankind, was betrayed by his favorite son, and ascended to godhood on the Golden Throne.
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