All the complexity and diplomatic maneuvering was just kind of dropped, and they made some weird narrative choices that amounted to character assassination of Paul. In the book, Paul is sort of the very reluctant villain of the whole story, but they basically cardboarded him and made him seem like he wanted mass slaughter.
Then there was the whole thing with Chani. Maybe the point was to elevate Chani was the "wronged woman" to give her a greater role independent of Paul, or to create some kind of romantic drama in a sequel. But there is also a strong plot purpose to the Paul/Chani/Irulan dynamic, and that was precluded by the choices they made instead. Bleh. Nor was the CHOAM/spice/Navigators, etc., interaction explained at all, which is kind of critical to explaining the "why" of the story.
As it was - my son who hasn't read the books - though the end was confusing and lacked context/explanation. He couldn't figure out how and why the Fremen were able to board spaceships to take them all over the galaxy for their jihad. A fair question.
Also, I didn't like Stilger being made into a buffoon - I don't think that kind of humor worked well because it kind of diminished the Fremen. There also was a key moment with him at the climax where he asks Paul "what's next", when Paul's whole problem was that a galactic jihad already had become inevitable at that point. Stilgar's question made it seem like there was still a chance for Paul to avoid it when there wasn't. So Paul then calling for the jihad made him into a really bad guy - like he actually wanted it.
I did loved the way Jessica was handled, even though I disagreed with the time compression and Jessica still being pregnant at the end. She seemed more than just "Paul's mom", which was good.