Of the two movies, Dune 2000 seemed more accurate (it's been awhile since I've read the book so I can't remember details) but less in tune with the book's feel. For all its many flaws (and grotesqueness), 1984 Dune carried a flavor of vastness, otherworldliness. There's something to be said, I suppose, for not having everything spelled out completely.
Dune 2000's biggest plus is William Hurt, who I like, mostly for his quality of understatement. I could almost believe that the guy was a threat to the Emperor-- almost. In fact, the story of Dune holds together fairly well (and is surprisingly simply once shorn of background noise: ousted prince retakes his kingdom: very Campbellesque).
Still, I wasn't terribly impressed with Dune 2000, and I disliked the precocious child (Paul's sister, end of movie). I'm not a big fan of solutions that use precocious children and yes, that means I never cared much for Wesley from Star Trek (although I never loathed him as much as other people). I started reading a book in the middle of watching Dune 2000 and frankly, I'm not sure it mattered what I missed. Heros run around in the desert. Scene cuts to the sneering Baron. Heros run around in the desert somemore. And I think the problem, really, is that haircut. Because it stopped mattering to me at some point that this guy was Mr. Cooler than Cool.
Ironically, I never believed in the 1984 Paul because he went on looking boyish and charming with his carefully hairblown dos. But at least he stayed human. Paul 2000 with his "I'm so in touch with all that space out there, I have to look like it" couldn't sustain my interest, which is vital if one wants to care (at all) whether the Baron gets Dune or not.
The point being, that for a film to work, the audience has to be invested in the outcome. And if, as also happened to me with Titanic, you stop caring about the protagonists or, worse, start rooting for the antagonists, the film has failed. (Unless you get into the history of the thing and start watching the movie for flaws, which is also what happened with Titanic.)