Checks thread title - spoilers ok - however, I'll code them anyway.
The Bene Gesserit being the primary villains is more subtle in the books, but they have sound motives for their plans within plans. Paul is a villain, but he has no option but to be one. He's a clockwork Muad'Dib on rails and he knows it. He shouldn't exist and Jessica is to blame for that. She is also more of a villain as she uses her unlocked other memories to seek revenge on the Harkonnens and the Emperor. Billions of people will die on may worlds in the holy war that has been unleashed. The reason for this jihad or struggle is made more plain in this movie than in the book. As for Alia being as yet unborn, but still able to enforce her will, I think that works better than having a small child kill the Baron with a Gom Jabbar. If the adaptations ever get as far as Children of Dune, it will make it a little harder perhaps to explain Alia's fall into abomination.