Dune (the book) had a real problem with scale. It's kind of Macbeth level political drama set over the entire galaxy and across worlds, but each house has like 500 soldiers and a mule. It's not at all interested in the details of numbers, figures or fleshing out the nitty gritty details of logistics. The Harkonnen sneak attack kind of just happens off-screen, so to speak. I think the film does a better job of visualizing the scale of things, and then only just barely.
It's also pretty clear the Kwisatz Haderach is supposed to be a combination of the "male" (Mentats are always male) and "female" (Bene Gesserits are always female) as Paul explicitly receives Bene Gesserit and Mentat training, something the film kind of blurs over. IE, the intuitive female combined with the analytical male. The whole Fremen prophecy thing is also specifically seeded by the Bene Gesserits centuries ago to "direct" the path of the Fremen along lines they predetermined, which makes everything feel much more deterministic. There are also "pseudo" Kwisatz Haderachs around, guys that almost-kindof reached that point but didn't quite make it; there is a strange character at the end of the novel that stands there and acts by not acting, whom you never saw before and never see again that's one of these.
There's definitely a lot of mysticism. Aside from the obvious parallels to Islam (the story of) and lots of vague religiosity (which it never directly confronts one way or the other) the Bene Gesserit are "powered" by genetic memory, which is at best Jungian and at worst complete nonsense. Guild Navigators imagine their way through space, and the Mentat can compute figures as well as a computer. It's kind of cool to think about directed evolution but, again, the book doesn't really flesh this stuff out. There's also a definite hippy undercurrent of "drugs open the mind, man" vibe to everything.
In other words, i was surprised that the film did some things better than the novel, imo, and that the novel wasn't the perfect gem of SF i had expected it to be.