There is no getting around it: the film suffers greatly from pacing problems. The extended version, using matte painting and a voice-over backstory, actually sets a compelling stage for the story. Right off the bat, the first scene has the Spicing Guild telling the Emperor, offhandedly or pointedly (depending on how you interpret them beating around the bush to get to it) that a person of little interest to the Emperor should be killed. That suggestion sets about the chain of events for the story, but after that first scene, the film grinds to a halt. We spend the next 40 (!) minutes showing life for the this house Atreides, the Baron Harkonnen hamming it up like a mad dog, Sting preening like no one else, and foreshadowing aplenty. If you stay awake, it's mildly interesting, but aside from the Gom Jabbar test (which is excellent), there's very little that actually happens.
After the arrival on Arrakis (aka, Dune), the film speeds up. In fact, all remaining sequences speed up, as if a producer looked at the film to the point and said we can't afford to spend another hour in setup. So, the Atreides' "getting to know you/inevitable countdown to betrayal" time is only 30 minutes. Then we have lots of explosions and the death of Duncan Idaho -- Richard Jordan we hardly got to hear you chew scenery (luckily, Patrick Stewart fills in on that not nicely -- almost a characature of himself).
After the escape of Paul and his mother, in what feels like a hot second, they go from strangers in the Fremen (aka chosen people) camp to revered members. This is a variant of the pacing problem from the other end -- a little more time and exposition would have been nice so that it doesn't feel incredibly forced that the Fremen ("who don't give their loyalty easily" as Duncan Idaho intones earlier) embrace the foreigners in a few seconds.
Pacing problems aside, the way the religious jihad angle / super-being / prophet from God tale is handled comes off as very fantastical and hasn't aged well. Given the state of affairs on our planet these days, when the hero of the story warns that anyone who stands against them is standing against God, it's chilling and not very empathetic. "And his word carries death eternal... to those who stand against the righteous." Sting's famous, incredulous reply "The righteous??!" sounds a lot like what I'd say against such a person. The way the prophet's rise is handled comes all too close to too many false ones on our own planet, promising eternal suffering for those who stand against them. Fear is a staple of most religions, and it is distasteful in every case. Makes me wish Sting had not just been boasting when he said "I will kill him."