First, I want to say that I really liked the movie. I think I gave it an A-. It could be better, but I am very interested in seeing a sequel (or two), and am interested in seeing more elements from this one (maybe an unofficial director's cut, since Ridley seems ambiguous about a different cut given the multiple quotes he has had about deleted scenes).
Although I'm not sure I want to see a film where Noomi Rapace and Fassbender's head visit the engineers' homeworld and engage in a 2 hour flute conversation about the nature of existance...
As a narrative thread it falls at the first hurdle because it seems to have been written backwards so it doesn't feel organic (pardon the pun) it just feels really contrived because we have no idea why David infected Hollaway in the first place, so what we're left with is the only reasonable conclusion: David infected Hollaway because how else would Shaw kill the engineer at the end...
How can we not take it as an Alien film?...
I have to disagree with several points here. While I agree there are a lot of bits that should have been different (the scientists should have done more surveying/quarantine setup/better choice of crew), they weren't, and I think that the movie works well in spite of these nitpicks. Additionally I would be really surprised if there wasn't a scene in the original screenplay, the storyboards, or even in the deleted scenes that show at least some surveying. Given Ridley's attention to detail, I find it hard to believe that he would let them get by with just stumbling across the alien site in the first 5 minutes. I think it just got cut out for pacing and to keep the wonderful visuals contiguous. (Anyone out there have the script? Did Greg Cox work on the novelization? Is there a novelization?)
The biggest real problem is the inconsistent actions: mainly the biologist and geologist flaking out and the biologist not being interested and then being really interested in alien lifeforms. But minor side characters being unimportant and killed off, I don't so much mind their characterization. Sure a perfect movie would have not had this problem, but this isn't perfect (unfortunately).
Some other points raised here and by others I think simply miss some of the key elements of the movie. David is experimenting - he doesn't inherently care about these people, he doesn't have empathy or other emotions or a "soul", so as instructed by Weyland he is trying harder to find the Engineers or their biological technology. He infects Holloway as an experiment to see what happens...not to have Shaw infected, to have a facehugger, to defeat the Engineer. Those just happened. You can call it coincidence, Checkov's Gun, a story coming full circle, or whatever you would like that the giant facehugger is there; but I don't think this element was poorly written, if you pay attention to character motivation it had a logical starting point.
Some other specific points:
1. Given the focus on thriller moments and body horror here, I don't think we will have a 2-hour sequel of people talking about philosophical ideas. Like this movie, we will probably get some initial mentions of these ideas, and some follow-up on them, but a majority of alien action.
2. Shaw and David don't focus on the c-section and the 'baby' because as soon as Shaw runs into anyone else afterward, she finds that Weyland is alive, there is still an Engineer alive, and they are going to meet him. Though important, the whole "science experiment" that David was running on Shaw pales in comparison with the potential to get all the answers. I think from that point out she is going with them for the potential to answer the big questions but is the only one prepared for what happens; she is the only one who realizes what is really going on, and how bad the situation is - everyone else is lapdogging for Weyland.
2b. I think the deleted scenes will probably have a lot of the little scenes that answer the little questions or show the small character reactions/interactions that are potentially missing in the final film (maybe including why the engineer head exploded...). Yeah, they tightened the narrative maybe a little too much by cutting down the run time, but it does focus the movie on the more important themes even if it does leave some lingering questions that put some people off. It isn't like we haven't seen over-editing with any other movies ever (Kingdom of Heaven, Metropolis).
3. This is definitely an Alien movie. It is not the straight-up horror movie that Alien was; it is not the action-horror movie that Aliens was; it is a philosophical scifi-horror movie. I think in this way it fits in perfect with at least the first two Alien movies.
One interesting item I have read: someone pointed out on the web that the scene where Fitfield (the geologist) returns infected is out-of-sequence from where it goes according to the script. You can apparently tell from some of the trailer footage that it originally occurs as the away team with Weyland is about to head to the alien ship, and that Shaw is the one who drives the vehicle over the body. I would really like to see this scene where it originally stood, because as other than an action beat, it doesn't serve much of a purpose where it is now.
I liken this movie to The Matrix Reloaded: a good follow-up (though a prequel) to an amazing movie, that expands the mythology, has lots of good visuals and a good overall movie, and leaves tons of very interesting questions for pondering. Hopefully, unlike the Matrix Revolutions, the follow-up movie won't completely drop the ball.