I liked pretty much everything about this movie. Things I would have done differently? Maybe some, but why should I mark points off for something not being the way I would have done it if I don't particularly dislike how it actually was done? That said, I'm not going to pretend to know more about movies than I do by being all uppity and deducting single random points. I'm giving this a 100%. Sue me.
It didn't feel formulaic to me. I never felt like something wasn't explained well enough to me or that I needed to see more in order to understand something. Instead of turning my nose up to the lack of suspense compared to 1979's Alien, I welcomed the fact that it was something different. I really liked the Engineers, and what I perceived to be their self righteousness. When they saw David, a non-organic copy of a human being standing there, look what one of them did. When they saw how humans turned out (more specifically, their choice of what to worship...or no longer worship), look at all the DNA-altering black sludge they packed in their cargo hold. Sorry if that feels like itisn't vague enough, but I am really trying to explain why I liked this without spoiling it.
Direct tie-in to the Alien franchise? Yes and no. Not right in front of your face like 2+2=4, but it gives you some puzzle pieces and shapes them just enough to allow you to see what they come together to create without actually fitting them together for you. It's the kind of vague reference that I was hoping for, with cool nods that did not compromise the individual identity of this movie. It's not just a set-up or a prequel, but it definitely expands upon an already existing universe.
If you're one of these high and mighty people that can't go see a movie without rolling your eyes at the sight of an American flag or a mention of politics or religion because of the fact that it might clash with your own set of beliefs, well...PLEASE check that crap at the door. There is something of a little religious tidbit here and there, subtle if you're a mindless pop culture zombie going to see a movie that has been heavily advertised - but interestingly used if you can allow yourself to enjoy it without being offended at the mere presence of religion within the plot. One of the two main characters does not let go of their faith, and things happen to go above average for that character compared to everyone else. This also relates back to my comments on the Engineers, relating to them in a way that I found clever. One of the things I haven't seen a lot of people touch on: "The search for our beginning could lead to our end." An end that apparently could have happened in the past, and for some reason did not? How did we get so lucky? Possibly explained by the belief of one of the main characters who contends that nothing they've discovered has any implications on their own religious views, while others feel differently about it.
I could go on a lot longer about this movie, but it's hard to do so without being more specific. I really enjoyed it, and I feel many others would too. My advice is to not be too nitpicky by comparing this too much to the Alien movies. Think of it being more like what Halo ODST was to the Halo franchise, or maybe Red Dragon to The Silence of the Lambs - same "universe," but not the same story. Good enough to stand on its own and have its own plot all for itself, but enough there that you can easily see how it is connected to the others.