This movie was released less than a week ago so I'll do my best not be spoilery.
I'm a huge fan of the Alien franchise. My overall feeling of blech for this movie has nothing to do with its connections to the other movies. It has nothing to do with the actors-- I felt everyone delivered their lines and characterizations very well. It has nothing to do with the cinematic effects, which were quite awesome. And it has nothing to do with how the filmmakers used this story as a medium to question human origin. That's typical of this kind of sci-fi.
To put it simply, the story movement felt forced and unnatural.
Critics of the critics, those in support of this movie, are saying that it's one of those films you have to watch a few times before you understand all the interwoven complexities. Which is fine, if it were true. I've seen plenty of movies like that. Inception, Sucker Punch, The Matrix... but all of them had something that Prometheus doesn't-- an organic plot flow.
What I mean by organic is that you can easily follow the story's movement from one point to the next, even if you don't yet understand all the details. The motives and decisions and actions feel natural to what you would expect. This doesn't mean there aren't any surprises. It means that in hindsight, everything makes sense.
Looking back on Prometheus, I'm still shaking my head in confusion over certain things. It just didn't feel right.
I can't really explain why I feel this way without giving away parts of the movie. But it all boils down to one thing, really. Understanding motives.
If a reader or viewer doesn't understand why a character is doing or deciding on a certain course of action, the entire story turns sour. And you can't prevent this by explaining motives. They have to be shown, and feel organic as the story moves along. Seamless.
One way you can pinpoint trouble areas is by enlisting the help of a trusted beta reader. I recently had a beta reader tell me that she was enjoying my story until my main character did such-and-such. After that, she lost her interest in the story and no longer felt vested in the main character's well-being or the story's outcome. In other words, she stopped caring about what happened because it didn't feel plausible anymore, because of a single course of action that didn't feel justified.
I took this comment very seriously, and ended up rewriting a good chunk of story to fix the problem.
What did I learn from this? You have to explore every possible line of thought, then shoot them all down except the one you want the character to use.
When I'm reading a book or watching a movie, the main thing that annoys me is when I can say, "Well why didn't he just do this instead of that? Then there'd be no problem!" I feel like, if I can come up with a realistic alternative on the fly, why didn't the writer think of that alternative and then do whatever necessary to make it impossible? Because if something is impossible, I won't question why the character isn't doing it.
You make things organic through their setup. So if you're having issues with the plot feeling unnatural and forced, work backwards. Start at the end result and ask yourself how many ways you can get there. The more possible paths you come up with, the more setup is required to narrow down the choices. Why would Bob go left instead of right? There has to be a reason, and that reason has to feel realistic to the character who chooses it.
In Prometheus there were reasons given for motives, but they felt rushed and shallow, thrown out at the last minute just to explain what happens in the very next frame. There was an overall lack of proper setup. Which is kind of inexcusable considering this movie is a prequel, meant to explain things we already know of in the other movies.
I know it is likely just the start of yet another group of movies, but considering that nearly everyone in this film dies (I don't think this is a spoiler because it's true to the nature of all the Alien films) it doesn't matter what happens in the next film, they won't be there. Their motives have to make sense now.
And I honestly don't think it would have taken much troubleshooting to fix this. A few bits of dialogue added here, a few unwarranted reactions cut there, and most of the issues would have been solved.
A satisfying plot has an organic flow. Organic = natural. So if someone says that something in your story feels off, unnatural, implausible, unrealistic... it's worth the effort to explore your other options. Either find a better alternative or clarify why the previous expectation is impossible.