On the positive tip, there are some incredible scenes (no spoilers, but I'm referring to a scene of heroic self-sacrifice, and a scene with a surgical procedure). Fassbender, Theron, and Idris Elba are very good, and Noomi Rapace is great. I think the movie's many flaws would be more apparent with another actress in that role.
Many things look great, but that's mostly because they look like Alien. (Oh, and by the way, this is a prequel to Alien – you can see the pieces shifting into their proper alignment – and I think that Ridley Scott's comment that it wasn't a prequel but that it "shares some DNA" was intended as a joke, given how important DNA is to the film.)
The problem is that, common DNA aside, this movie loses the great virtues of Alien (a defined space, a discreet and clearly-defined group of characters, a hidden menace, and a clear connection between the plot and the underlying meaning) and replaces with with a lot of different elements that don't hold together.
Do you want to enjoy it as a scifi adventure film? It's constantly poking you with its "I have deeper meaning!" stick. Do you want to think about the deeper questions? Some of them the movie doesn't answer, and others it is clearly leaving for a possible sequel, where (I have the feeling) they won't be definitely answered either.
When I failed to see this movie the first time, I saw The Avengers instead, and they have an interesting difference, and an interesting similarity.
The difference is that The Avengers has basically two ambitions: to entertain you for two hours, and to get you to want to see all the various movies which will follow it (more Iron Man, more Thor, more Captain America, I guess possibly some Hulk, possibly some Black Widow, and more Avengers). In that, with the caveats I wrote about before, it succeeds. Prometheus has more ambitions, but it succeeds at some and fails at others.
The similarity, and this has application to anybody who does serial storytelling, is that neither movie stands alone. The Avengers has to follow the four movies which preceded it, and lead into the ones that follow, and that constricts the options at every turn. Prometheus has to leave things in their proper alignment for Alien, and it also has to leave the audience wanting Prometheus II. [Later: and as was pointed out by a commenter here, Prometheus is also apparently trying to be a remake of Alien itself (there are quite a few plot points which are clear echoes of the earlier film).]
This is possible to do well, however (and a good thing, too, for me 🙂 ), and thats illustrated by Serenity (which is a better movie than either of these). Serenity had to follow a failed TV show (Firefly), so it has to take up plot threads and characters from the show, but it also has to bring in the audience that never saw the show (presumably the majority). It doesn't do this perfectly, but it does do it very well (I saw it before I saw the show, and am now backtracking to watch the episodes). The ending leaves the door open for more stories, but it does end, and quite satisfyingly. And, like Prometheus, it raises big questions, but it is comfortable with them (as opposed to Prometheus, which always has one foot in and one foot out), and it's clear how the themes relate to the plot.
One final point, which is that Joss Whedon and Ridley Scott are very different types of filmmakers, and therefore comparisons are difficult. Many people, including me, have compared The Avengers to Rio Bravo, and Howard Hawks is a good comparison for Whedon. Characters, timing, dialogue, acting, those are where he's focused. There is only one really memorable visual moment in Serenity, and it's an image of a person.
Ridley Scott is a different type of artist. There are some incredible visual moments in this film, and some sequences of sustained action and suspense that are beyond anything in The Avengers (or Serenity).
Joss Whedon will never give you the first few minutes of Blade Runner, and he wouldn't try. But Blade Runner holds together a lot better than Prometheus, partly because back then you could make a science fiction movie that didn't have to lead into sequels. (And, it should be said, Alien produced sequels, but it doesn't set things up for them. There's nothing in Alien that says, "Hey, we're leaving this in place for the next movie!").
At some point I may write about Prometheus and Avatar, which is an interesting comparison, but I think I'll have to wait, since it wouldn't really be possible without spoilers.