First things first, Prometheus is not, in any way, an Alien movie. Apart from lifting a lot of iconography from Alien itself, I don't even think it especially tries to. After all, what is an Alien movie anyway? The first is a brutally efficient little Haunted House in Space tale, and the second a blood-thumping war movie, and then it all starts to go downhill a bit. Well OK, a lot. Alien 3 and 4 are both terrible messes that occasionally spit out an interesting idea or scene but certainly don't "work", and then we're into the Aliens vs Predators stuff which I just can't be bothered to watch. Sure I may be missing something but falling back on nostalgia and slasher tropes (which is what the trailers look like) doesn't do it for me. But if you're a long-standing fan, I'm guessing that the big established tropes is what you're after, and Prometheus isn't interested in that.
What Prometheus does want to talk about, then is identity, and desire to know your origins, and the weird, unknowable horror of the gods. The plot revolves around a scientific expedition to a distant planet in search of extraterrestrials that may have been in contact with early human civilizations, "Chariot of the Gods" style. Once there, of course, everything goes to hell in a maze of conflicting agendas and idiot-ball juggling, as we come face-to-face with dark truths and deeper mysteries. It's these mysteries that are, I think, the spine of the criticism aimed at the film, as there is a near-Lovecraftian tendency to portray the Engineers and their technology as un-explainable, and so the movie doesn't even try.
Now, I liked this, mostly. There is a difference between a plot hole and something that simply isn't explained, and the whilst Prometheus hops across this line a few times either way, on the whole there is a "At the Mountains of Madness" vibe which I really liked. It also fits the films visuals, fierce contrasts between the shimmering technology of the human expedition and grey/black Engineer base and ships. Actually I don't think I can emphasize enough just how stunningly gorgeous this film looks at times; David viewing the Engineer's star map, the Prometheus coming into land, the dark recesses of the underground base-come-tomb. Scott has always been at his best as a visual director, and he shines here, especially in the films first hour, before some of the cracks start to show.
There are of course cracks - like I mentioned the plot relies a little too heavily on the unexplained, especially the "magic goop" which has one or two too many iterations. The final confrontation feels a little short-changed, although I mostly bought into it, and one characters death is beyond stupid; like something out a far less thoughtful movie. At times I wonder if there is a "Directors Cut" out there that adds in another 20 minutes, and just tightens everything up. As it is, some strong performances hold the character work together, especially Noomi Rapace, Idris Elba, and Micheal Fassbender.
Away from internet hyperbole, Prometheus isn't a triumph but neither is it a travesty. In some ways I feel it would have got a warmer reception without the Alien links, although the reuse of the striking imagery from the original film is one of it's strengths, it also undercuts its story. If Alien had never existed, I suspect we'd all like Prometheus a lot more.