The big question that most movies should set about to answer is, how can I make this experience worth 15 bucks (and 2.5 hours)? Movies that answer that question well and artfully are movies that I'm happy with. The biggest problem with Prometheus is that it set itself up to fail on this question by trying to make itself out to answer philosophical questions, bigger questions than a movie can answer. So the biggest problem with Prometheus is the ancient Greek problem of hubris. Funny how that works.
For me, this movie was worth it just to watch, and to explore a new world, and to find out some smidgens about how them nasty Aliens came to be. As such, it was well worth the 15 bucks. If only Ridley Scott and the writers hadn't made such a big fuss about how this wasn't really an Alien prequel, it was a separate movie, it was different and it answered big questions, etc. etc. etc. I think most negative reviews come from the expectations they set up for themselves. This movie isn't much more philosophical than any of the previous movies. It's about exploration, not philosophy. It may have some interesting things to think about in terms of human creation and mothers and pregnancy and things like that, but the other movies have the same level of depth.
In the end, I enjoyed Prometheus about as much and for about the same reasons as I enjoyed 2010's Tron: it looked really good and gave us some fascinating (and in the case of Prometheus, gooey and icky) passages to explore. Tron had its own aesthetic, Alien cribbed its from H.R. Giger, and I'm familiar enough with Giger's work that Prometheus didn't really look new to me. The science in both films combines a few interesting ideas with a bunch of ideas that are just not the way things work (bits in a computer having personality? in Tron; chemical facts such as rates of growth and the basic structure of DNA in Prometheus).
But even if it's more fiction than science, it still looks really cool. To me, that's worth 15 bucks. Just don't oversell it or certain critics will chain you to a rock and order an eagle to eat out your liver or something.