Some would (and have) said that these characteristics are a sign of a film maker who's lost touch with the material, maybe even the entire project. But this is David Lynch we're talking about here. If you hire David Lynch and expect to get George Lucas you haven't done your due diligence. Lynch wanted a world apart. Unrecognizable in some respects, nonsensical to a degree yet still 'real' enough to connect on a visceral, emotional level. He reaches back into art history's darkest, most evocative corners for inspiration; Hieronymus Bosch can be seen in the Freemen massing at the imperial gates late in the film, the floating grotesquerie that is the Baron Harkonnen has Francis Bacon oozing from his pustuals. The art direction in and of itself is worth the price of admission. The medieval-modern of the emperor's palace, the carved-from-solid-mahogany-and-covered-in-27-coats-of-laquer look of the Atreides home on Caladan; nothing is done half-way or overlooked for its symbolic potential. Case in point, the shoreline on Caladan is not some tranquil white sand paradise but a roiling, crashing, dimly lit tumult echoing the feelings of Paul and his family as they prepare to walk into the lions den of Arrakis. The Guild Navigator is the baby from Lynch's Eraserhead all grown up. The great hall where Paul declares "Long live the fighters!" is more than a little reminiscent of H.R. Giger's 'shafts' drawings of the 60s which were, interestingly, a record of one of his recurring nightmares. (Giger himself was hired on to help with earlier, unsuccessful attempts to bring the story to the screen and echoes of his hand are faintly felt at various points throughout the film.) Dune is also replete with many of Lynch's recurring themes: appearance vs reality, grinding, steam-belching machinery, mutation either genetic or man-made, the complex and powerful nature of sexuality. Even his semi-infatuation with the post wars years can be seen in the bulbous spacecraft that bring the members of House Harkonnen to Arrakis as well as the Guild Navigator's "tub"; both of which look like the mutant spawn of a 1950s Buick.
Why all this emphasis on the look of the film over the script/storyline? Because in Lynch's reading Paul's journey is not a political one so much as it is an emotional one. Because of this the emotional landscape Lynch creates with his imagery is crucial to telling the story as he sees it. More important, in fact, than fleshing out the back-stories of particular characters or wallowing in hours of exposition in an effort to clarify details of the myriad political intrigues. As a result Paul's life as depicted here is, like ours, nothing if not a series of vaguely connected occurrences that sometimes make sense and often don't and its how he deals with the stew of emotions engendered by these occurrences that will determine what position he rises or falls to within his own milieu. Were he not buttressed by vague yet powerful feelings of a fate largely beyond his control he'd crumble at the task before him. Instead he assembles himself like a grand jigsaw puzzle out of the disparate elements of his emotional life and only when he finally feels his external reality match up with his internal dialogue is he able to proclaim "Father! The sleeper has awakened!" and cast his fears aside. His apotheosis is not the result of outmaneuvering his opponent on the battlefield, but instead of creating an emotional harmony between his internal and external lives.
So focusing on where Lynch may have failed to literally illustrate Herbert's words is, to me, a waste of time. If literal is what you want rent the scifi channel's version from 2000. I take it as a given that Lynch has discarded much of the book's literal narrative in favor of emotional narrative and appreciate the lengths he's gone to to recreate with images Paul's emotional saga. Anyone uneasy with this aesthetic choice will probably be unhappy with the resultant film, feeling he's betrayed Herbert. But film is its own medium with its own possibilities and limitations and Lynch has made a career out of exploring its possibilities. Dune is no exception.
Dune is not a film that requires the viewer to suspend their disbelief. On the contrary Lynch insists that you believe that there are truths which transcend reality lurking in the subconscious of every man and that only a fool ignores them. When the final credits on his expansive, beautiful, unsettling epic began to roll I didn't feel as though I'd reached the end of a movie, I felt like I was waking up.