So about those shortcomings . . .

Commenting specifically on Prometheus' character development is futile, because so much of the story makes no rational sense.  As others have noted, the film's two hours don't comprise a plot as much as a lurching progression of scenes, each predicated on the convenient stupidity of its characters, each bearing little rational relationship to what preceded it. So here are a few instances that littered this film that I haven't seen discussed elsewhere.

First, a very easy one

Let's say you're a cocksure scientist on an interplanetary expedition and your hubris overwhelmed any reasonable utilization of personal protective gear and—lo and behold—you find yourself infected with a space bug. (Yes, ironically, it's not your taking off your helmet that did you in but your willingness to drink booze that just had a dirty robot's finger in it. But you're too dumb to consider that anyway.) This infection is not just a sniffle or a cough. It's serious. You're going to die, and you've realized the sooner, the better.

If you are ready to die, what's your preferred mode? Roasting in a spacesuit until the flames finally reach and incinerate your flesh, or . . . anything else? Like, oh I don't know, asking the Captain to get one of those shotguns and put a round in the back of your head? And while you're at it, since you are doing this for the good of the crew, why don't you take that business off the deck of their ship? You've already made the round trip to the ruin; you can stumble away for another twenty feet or so.

In that scene, notice how Vickers perceived Holloway as a threat--”Stay back!”--despite the fact that Holloway is clearly surrendering himself to her. The glaring contrivance of her misperception is a manipulation, attempting to justify the brutality of what Vickers does to Holloway. Oh, the melodrama of it all.

What is Shaw upset about?

Prometheus' mission only happened because Shaw and Holloway convinced Weyland that LV-223 is the source of human life. Indeed, the audience saw the Engineer consume the black goo to contribute his DNA to Earth's ecosystem. And after their first trip to the ruin, Shaw confirms that the Engineer's DNA matches ours. It looks like Shaw's hypothesis has been confirmed. So why does Shaw conclude the Engineers are out to destroy the Earth? Because Captain Janek told her the place is a weapons factory? He's just a pilot; Shaw is the archaeological expert who's spent twice as long at the site. Is it because of the bad outcomes with Fifield, Holloway, and her first shot at motherhood? If one went into any hospital on this planet and handled its materials with the carelessness of Shaw's team, one could experience similarly deadly outcomes. That doesn't mean the hospital is a bio-weapons facility. Shaw is supposed to be a character of conviction, yet she's not even willing to use logic to examine her central conviction which is the whole purpose for the mission and, thus, the film.

Sure, David made the veiled threat, “Sometimes to create, one must first destroy.” But there's a problem with that, too. Let's assume that David is perfectly fluent in the Engineer's language. (Though based on the reception he got the first time he spoke to a native speaker, maybe he's not quite as fluent as he'd have them believe.) Let's even assume David knows that, prior to going to sleep, the Engineer's intention was to go to Earth and release the black goo to wipe out life as we know it. Even if that's true, there's still a problem. That's because those plans are two thousand years old. And sleeping away two millennia has a way of making you reevaluate. David and certainly Shaw have no way of knowing the Engineer's intentions upon waking up. And there's no reason to think those intentions are the same as they were two thousand years ago, even in the unlikely event that David perfectly understood those intentions.

(Also, why are those Engineers in sleep chambers anyway? Sleep chambers on spaceships are meant to preserve resources on extremely long flights. But this ship hadn't left the ground. Were they just that sleepy?)

For the characters on Prometheus, Shaw's evidence and logic should seem far too weak to warrant their suicides, especially when they could radio Earth which, presumably, could deploy a fleet of warships to intercept the Engineer. For the audience, it appears that the only writing that establishes the Engineer's threat is the tag line on the movie poster, “The search for our beginning could lead to our end,” because the clarity of that threat certainly isn't established within the story itself.

Back and to the left

Once the Engineer's ship does take off, it moves in one direction, say, north. Shaw and Vickers are moving in the opposite direction, south for our purposes. As the Engineer's ship continues flying to the north, it is rammed by the Prometheus (flown by those jolly, suicidal copilots), which is also moving to the north at an even higher speed. Yet once the collision occurs, the engineer's ship does not follow a northerly trajectory. Instead, in complete defiance of Newton's laws of motion, the ship falls backwards, to the south, over Shaw and Vickers. (If you've ever been in a car that was rear-ended, you know that your car lurched forward, not backwards.) In this “science fiction” movie, the science is getting checked at the door.

And while we're talking about defying physics, I invite you to get a disk-shaped object, say a coin or a washer, and toss it in a random manner and see how many times it lands, rolling on edge, like the engineer's ship did. The answer will be practically zero.

Crafting credible characters requires exposing them to limitations. The world in which they live must seem realistic. The character's behavior should be plausible. Extreme behavior is possible, but the writer must earn the credibility of such behavior. (See Pulp Fiction's “The Gold Watch” for an example of a writer earning extreme behavior from his character.) In all of these matters, Prometheus failed completely, and what results is a genuine insult to the audience's intelligence.