It captured some aspects of the books, but diverged heavily in some baffling ways..
1. Everything with the Harkonnens is gross, it wasn't like that in the books. This aspect alone made the movie hard to take serious.
2. the stupid blaster guns that were added
3. the ending was complete nonsense and did not come from the book
Not sure how you can say this new movie is missing stuff, it appears to be a much more accurate retelling of the book to me.
Lynch's Dune can be bewildering coming at it without the context of the book, but that aspect of it is frankly just something you get used to with Lynch's works, and like you said its filled with so much oddness and detail. The hulking Heighliner spacecrafts, the mutated ghoulish guild navigator, the fascinating cave-like imperial palace set, the manic cyst-covered Harkonnens. I've never understood why it gets a bad rap, I think it's a hugely underrated film that did a wonderful job capturing the strange universe of Dune.