In fact I've heard a lot of references to Messiah being written by Herbert because he didn't like the reception to the 1st book. I

Yeah. That's based on an interview that Villeneuve gave, when he was asked why he made the character changes that he did. It isn't true. Herbert never said anything like that, in any interviews, or in any of the supporting literature that he wrote for the series.

In fact, Frank Herbert himself explained in an interview back in the 80's that Paul's story was always intended to be spread out over the 1st three novels, and went into a lot of detail about Paul's character arc. That interview directly contradicts everything that Villeneuve has claimed about Herbert's writing process.

Paul's character was never intended to be seen as the bad guy, as Villeneuve claims. He was a tragic hero. In the 1st novel, he was intended to be seen as the "perfect leader". Raised to be wise and just. He genuinely loved his family, and his people. His intentions throughout the 1st novel were meant to be as altruistic as possible, in that he did everything he could to avoid the bloodshed that he saw in his visions. But, even Paul's supernatural ability to see the future couldn't give him a way of avoiding the war that would eventually be waged in his name. In a very real sense that outcome was inevitable, and he was trapped by it.

What the overall story was meant to capture, was that no matter how "good" or "well-intentioned" a leader is...it is impossible to create an outcome that satisfies every member of your society, or avoids all potential harm to those who live under your rule. There are no perfect solutions in politics...only a long list of compromises that inevitably leave some people feeling betrayed. Sacrifices always need to be made in order to ensure certain outcomes are achieved.

Then there's the idea that the "greater" the leader, the more bloodshed they tend to leave in their wake. Human history is full of "great leaders" that were also responsible for the worst atrocities the human race has ever seen. Even a "perfect leader" like Paul, was no exception. Change often requires blood to be spilled. The greater the change, the greater the bloodshed.

The moral of the story is, there are no "good leaders", only those that try to achieve their goals with the least amount of damage being done. But very often, the "greatest leaders" in history, are the ones who are willing to do terrible things in order to "do what's right".

This is where Villeneuve's misunderstanding comes in, is h thinks this makes Paul the "bad guy", instead of making him the tragic hero who tries and ultimately fails to "do the right thing" by everyone.