I disagree completely, that movie was full of complete plausibility issues. I wanted to love it, but it couldn't get basic non-sci-fi things right.
Why would someone build a medical machine that can't operate on women? Why would they then give that machine to a woman, who is sort of important since A) she's related to Weyland and B) she's the commander of the ship? Why did no one care that Weyland was alive? Why did no one care when he died? Why didn't anyone run to the left instead of straight when escaping from the spinny death ship. Why did the biologist who likely had years of experience assume it was safe to remove his helmet on an alien planet solely because "well I guess there's oxygen? The fact is, aside from tons of unexplained loose ends (which I can appreciate, sure, they don't have to answer everything), it fails the "are these characters believable and is this at all plausible within the context of the world that has been set up?"
Also, I really don't think you're being fair. You've basically said "if you don't like the movie you either don't get it or you're mad it wasn't an Alien prequel (even though it was, though again, that wasn't my problem with it)." Why can't I dislike the movie because it was full of plausibility (within its own context) issues? I've seen that Prometheus Explained video, and it does not explain the complete lack of believability OR most of the actual issues people take with the movie. In terms of how the characters behave, the movie is utterly unbelievable. If you want to talk some sci-fi that doesn't make things obvious but still makes sense in its own context?
I actually meant to say Sunshine, not Blade Runner. Although Blade Runner is a great example, too.
EDIT 2: And I say all of this as a person who thought the movie was mildly enjoyable-- at least until I started thinking about it. Kind of like the ME3 ending, but I won't get into that ^^.