At this point we're going to have to make peace with the fact that Ridley Scott is done making good movies. He's just making movies that look great, and he's not terribly concerned about things like plot or character or thematic coherence. And if you accept that, you can enjoy Prometheus.
Prometheus is a movie that challenges our very concepts of what a good movie is. There is no way to deny that on all the levels of craft - design, lighting, cinematography, editing - Prometheus is a huge achievement. And the 3D is a wonder, a truly immersive use of the much-maligned gimmick. In the past I've said that only masters should use 3D, and Scott is certainly a master, and Prometheus supports my thesis.
On all the technical levels Prometheus is a great work. But there's more to a movie than that, and when it comes to the script and the acting the film falls flat on its face(hugger). Even the most cursory thought about the movie reveals plot holes, unbelievable character motivations, and lapses in the most basic storytelling. On this level Prometheus is a bust.
But what if you approach Prometheus as an experimental work? A movie where narrative and character are secondary (or tertiary) to technique and style? In that case the film works. It isn't like Prometheus is ever a slog to sit through, it's just aggressively stupid from end to end. It's a movie that is made to be seen on the big screen, and there is a certain joy that comes from seeing a film like this in the best presentation on the biggest screen.
This sounds like it's veering dangerously close to 'turn off your brain,' but I don't think it does. The movie remains stupid, and to ignore that is to ignore base reality. But the movie is also beautiful, and not in some kind of 'kewl' way. It's awards-worthy in its visuals, a film that is a work of art when it comes to what goes through your eyes. I think Prometheus is a true work of cinematic art. It's just a profoundly dumb work.
So I believe you should go see Prometheus this weekend, in 3D. IMAX 3D if you can. Expect to be exasperated with how poor everything that isn't the visuals is, and you'll be set. But as you're grumbling about the dumb scientist who last scene didn't want to meet aliens and the next scene is trying to pet an obviously dangerous alien snake, enjoy the art design of the scene and the slimy reality of the creature. Enjoy the depth and the evocative color palette. Keep your brain on to really appreciate and enjoy the good work being done... and to recognize the bad work that went along with it.