My younger self had legitimate complaints, and also failed to appreciate some of the subtleties. Let's debate.
Younger me: "The good guy just kills all the bad guys with no problem."
2012 me: "What makes you so sure he's the good guy?"
Granted, the story structure is one that certainly makes Paul Atreides the protagonist. But if you look at everything in the movie, nowhere does it say or even indicate that the Atreides family are inherently good. Granted, the Harkonnens like to torture animals, and they're all gingers, which is good enough to define their evil if you're named Eric Cartman. So their rivals who do nothing quite like that may seem better, even though they're secretly developing sound weapons. But part of what I like about the movie now is that there are no good guys in it. Everybody's hands are dirty, and it seems clear that if the film series had been continued, Paul would have amply demonstrated his flaws later on (not having read subsequent books, I don't know for sure how that suspicion plays out). The fact that he can't just kill Feyd, but must then use his divine power to split him apart, suggests absolute power corrupting absolutely.
Every spice you take, every dune you rake, I'll be watching you
Younger me: "He falls in love with this one girl just so they can have some kissing in it."
2012 me: "Yeah, pretty much."
Seriously, I imagine Chani actually has a story purpose in the books, but here, she's a prop just so Paul can kiss somebody. His line "I've always loved you," based on the fact that he fell for her in advance in his dreams, is totally lame as it plays.
Younger me: "He has a voice that can make them do anything."
2012 me: "It's more limited than you think."
As a kid, I totally misread the scene where creepy kid Alia (Alicia Witt, in her very first role) lures the Baron close to her. She isn't actually using the voice, but she is secretly wielding a poison talon. The voice, like the Force, seems to only work on the weaker-minded in limited situations.
Totally hot nowadays. We'd never have called it back then.
Younger me: "It's trying to be like a Bible story or something, except Jesus didn't kill like that."
2012 me: "Actually, that's the point, and the director seems to know it."
I'm aware that in the books, the Messiah prophecy turns out to have less-than-mystical origins. The film doesn't make that apparent, but there are very subtle hints - if the characters would stop thinking out loud so much, you might be able to stop and see them.
All that aside, there are definite fingerprints of Lynch to be found. The entire subplot of creepy preemie Alia, including in-vitro shots of the fetus becoming sentient (how was this not R-rated, again?). The clitoris-face of Carlo Rambaldi's amazing Third-Stage mutant. Paul's dream sequences, which cleverly use '80s technology in a way that doesn't look dated (even the CG Battle Shields fight looks weird rather than old, which is good). The way Irulan's face fades in and out when she delivers the studio-mandated exposition at the beginning. I do think it's the only Lynch movie where somebody doesn't have a massive crying scene, but I could be wrong.
Yep, THIS is David Lynch at work
The production design is still holy-shit amazing. And I love what's being set up here: a full-on sci-fi universe fleshed out on a grand scale that's predominantly dark and perverse is a radical notion, one that the Riddick movies haven't quite managed to realize either.
But MacLachlan, however much he may have won me over since, is still a terrible lead. He's fine as a dorky heir, but once he starts talking about "the Weirding Way" (a.k.a. martial arts) and being Messianic, he sounds like Derek Zoolander. He wasn't ready to star in a big event movie, and it showed both then and now. Oh yeah, the guitar riffs on the soundtrack by Toto are badly dated as well, though Brian Eno's main theme holds up.
With that said, I suspect the way to watch it henceforth will be with foreign-language audio. The incessant talking will seem more profound that way.