The more I think about it the more I like the "bad" parts of the script. The movie is about the subversion of faith/expectations, both in plot and in theme. The characters IN the movie aren't the only ones going into this with expectations that will be turned on their heads!
It's a brilliant deconstruction of/tribute to pulp sci-fi in the same way Cabin in the Woods is a brilliant deconstruction of/tribute to pulp horror. The big difference is Prometheus doesn't wink quite so openly at the audience and allows itself to indulge in its genre rather than just comment on it. Prometheus allows itself to be beautiful at times and genuinely horrifying at others without a hint of irony. Cabin in the Woods never does. Cabin's a lot funnier, but Prometheus is still pretty funny. The guy in charge of the maps getting lost is funny. The biologist teasing an alien snake and being the worst scientist in years is funny, especially since his writing and attitude set him up to be the Ian Malcolm of the film, not the bumbling sidekick to the guy who smokes Space Weed and then gets killed immediately after. These aren't plot holes, they're satirical subversions of what the audience wants/expects.
David plays the role of both the director and the protagonist villain. He's Ridley Scott commenting on the silliness/wonder of the genre but he's also Richard III. The film explicitly says, "Yes, this is the theatrical character" from his first scene. He's the best character and Michael Fassbender plays him perfectly.
I don't know if I'd recommend this movie to many people but I think it's one of the best I've seen in years. Instead of getting worse every time I think about it (Avengers) it gets better!
I also think it may be a better film than Alien.