It's extremely valid to talk to Harper. He worked a lot on the movie's spine and shape. John Logan may be Ridley's pet writer but he is far from infallible (see: Star Trek: Nemesis, earlier versions of Gladiator, etc).
It seems like any time they found something more in-depth that could've helped the film's story or characters Ridley took it apart to see how it worked, then left it on the worktable. I'm curious about the mention of a version where Shaw is offed right away, Hicks.
There are several great sequences in AC, and the production spared no expense; most of the first 20-25 minutes on the ship works for me (sans the painfully blatant bit where Oram awkwardly exposits on his religious character which goes nowhere in the final film), as does most everything til David takes them to the citadel. Once there it becomes a rolling disaster. Elements of the Walter/David sequences work, others are laughably pretentious even for someone with a high tolerance for Ridley's fascination with the artificial person. Nothing about David's connections with Shaw and Walter's with Daniels, or David's sudden adoration for Walter, makes sense or is properly explicated. The bombing sequence is dropped in as a sliver of a larger sequence and makes little sense on its own story-wise despite being visually grand. All the movie leaves you with is "and we killed everything from the last movie". To say nothing of the hilarious bit where David wails, "it trusted me!" And the alien developments are awful, as is David pawing Daniels; 'is this how it works?' Yes, we remember Ash and the magazine. That was a hilariously clumsy, stupid callback.
Great actors, gorgeous design, great creatures. Several great scenes, as mentioned. (The medbay sequence is excellent from arrival to explosion, one of the best in the franchise, suffused with dread and horror.) But overall easily the weakest film in the franchise for me next to A3 or AR, both of which have merits but are supremely flawed. I actually prefer AR; it knows what it is. This film is caught between retreading old ground and Ridley's private obsessions. Talented/intriguing people with connections have no characters (Lope/Hallett, whose relationship is offscreen; the winning Rosenthal who is spunky but gets nothing; sardonic Upworth who largely exists to die on the USCSS Camp Crystal Lake in the last 15 mins) or are killed very quickly (Faris, Karine). Waterston is sweet and tough as Daniels but devolves into a Ripley clone in the rushed second half. The classic alien is utterly unneeded and basically rumbles along in a straight line as soon as it appears. It's fodder now. Not scary. The movie is a ritzy fan service-heavy, pretentious Friday the 13th. I suspected it would be deeply flawed but I didn't know it would be quite this disjointed, messy and confused in its second half.
I'd never have been onboard with this particular story or wiping the slate clean on Shaw and Prometheus, but completely wiping out Noomi Rapace's screen time (right down to re-masking her face in the holograms post-test screening) feels vaguely punitive. Imagine the gravity of the drama if it had another 20-30 minutes, and Daniels or Walter had discovered David's 'beloved' Shaw sick or dying - infected? - telling them to kill her and destroy him. To say nothing of helping the overall pacing and characters as mentioned.