So if those two acts represented the whole of Alien: Covenant, I'd enjoy it but probably be pretty down on the story as trying too hard to be both Prometheus and Alien without really showing us anything new. There's some good horror set-pieces and fan service, but outside of that, it's pretty anemic. However, the bulk of the movie, the second act, is where Alien: Covenant is actually great.
This is the story I think Ridley Scott wanted to tell, full of dark meditations on the nature of creation and a clever recontextualization of the Xenomorph. It bears noting that Michael Fassbender steals this act, chewing up the apocalyptic scenery as David and acting as his heroic counterpart in Walter. I know a lot of people love to rag on the flute scene with adolescent giggling ("He said 'fingering,' teehee!"), but it's one hell of a scene. Not only is the dialogue dripping with subtext, but it's a long, continuous shot of two Fassbenders that is utterly seamless. It lays out the entire conflict of the story as being a battle for the android soul, about whether creation is a benevolent expression of evolution or a god-killing act of self-destruction, as set up by the Weyland prologue. Of course we know that David has to win this battle, which is as existentially bone-chilling as the Xenomorph is instinctually terrifying.
It's supposed to be weird and uncomfortable
Granted, the movie does ask you to accept the fact that Shaw died between movies, which is disappointing, even if, like me, you don't particularly like her as a character. And yes, Oram goes from face hugger to Xenomorph in record time, which feels pretty disrespectful to the canon, but I can forgive that because the David-versus-Walter fight and the Xenomorph scenes are absolutely friggin' awesome.
Now, taken as a whole, the film does present some unique flaws that deserve attention, not the least of which is its disjointed nature. There's also a palpable lack of a protagonist, no matter how much the movie tries to frame Daniels as the heroine. Each of the characters is saddled with profound loss and grief right off the bat, which really prevents much in the way of relatable character arcs in the handful of hours that make up the majority of the story. You can kind-of make the case that Daniels learns to move on from her grief by the end after she fights off its personification in the Xenomorph that pops up aboard the Covenant, but I feel like a bullshitter just for writing that sentence. (Besides, Aliens covers that ground far better.) From a strictly academic, narrative-dissecting perspective, the protagonist should be David--with the movie charting his course from a lost soul to a god--but the movie never really lets him take center stage, even though Ridley Scott obviously wants him to. Hell, outside of the prologue, he isn't even properly introduced into the story until the fifty-four minute mark.
The two best human characters
But okay, I've discussed the narrative to death. What about the filmmaking itself? As with Prometheus, there is some stunning cinematography on display, but a lot of it does get washed out by shadows, rain, and darkness (which is appropriate to the film's tone). The music does a good job blending the themes of the original Alien with those of Prometheus, but it isn't really notable on its own. The design of the Xenomorph--okay, technically, the "Praetomorph," but whatever--is absolutely incredible, though, probably the best-looking adult Xenomorph since James Cameron's. (The chestburster standing erect and outstretching its arms is admittedly pretty stupid and pretentious.) I even like the Neomorphs, especially the infant versions, and I'm glad they went with pale white instead of the deep blue of the so-called "Deacon" from Prometheus. The special and visual effects are also pretty incredible, with a brilliant mix of practical and computer-generated works that are sometimes hard to differentiate. There is one wonky bit of compositing when Daniels is fighting the Xenomorph on top of the makeshift dropship with the sunlit CG landscape sweeping behind her, but that only stands out because it is the exception, not the rule.
As for the actors, many of them do a commendable job. Katherine Waterston is fine as the Ripley stand-in, better than Noomi Rapace's version in Prometheus, though of course nowhere near as good as Sigourney Weaver. Billy Crudup is great as the bumbling, insecure guy forced into a leadership position, and though I complained a few paragraphs ago about his line where he says he's being persecuted for his faith, Crudup's performance makes me think the guy genuinely believes it. Danny McBride is absolutely wonderful as the down-to-earth pilot in the cowboy hat who is willing to sacrifice absolutely everything when he hears his wife's in danger on the planet surface, so wonderful in fact that I'd have prefered his character be the focal point rather than Waterston's Daniels. The head of security, Lope, played by Demian Bichir, is pretty endearing, too. Everybody else, though, is fairly forgettable, with admittedly undercooked characters that are little more than alien fodder.
James Franco's finest performance
What I appreciate most about Alien: Covenant are its horror elements and its tighter thematic focus. The characters may be a little thin, but they don't feel as two-dimensional, inconsistent, or cliché as the characters from the previous two films, nor are any great actors wasted on them. The plot, though disjointed, doesn't rely on nearly as many frustratingly stupid character decisions as Prometheus does, and the subtextual implication that the Engineers are seeking vengeance for the killing of Jesus has thankfully been memory-holed. (If you don't know what I'm talking about, it's probably for the better.) I like where Ridley Scott was going with the series, and I absolutely adore Michael Fassbender's performances as both Walter and David. Sure, a case could be made for the Xenomorphs not needing a backstory, but I appreciate how this movie tries to organically grow them out of the disjointed wreckage of the previous film.
Perhaps Alien: Covenant was doomed before it even came out. I truly believe a lot of people decided how to feel about the movie before they had a chance to actually see it, and I suspect those who hadn't were easily misled by a dishonest marketing campaign focused entirely on the film's final act. The movie doesn't do enough to satisfy those hankering for a complete rehash of Alien, but it is a welcome return to horror that is direct in its ambitions and adept at its execution. It is better than Prometheus on almost every level, and it is certainly closer to what the franchise should be than the bleak Alien³ or the confused Alien: Resurrection. I sincerely don't understand why the movie is as hated as it seems to be or why it has a lower aggregated rating with both audiences and critics than Prometheus. It's not a perfect movie, but it's much, much better than its reputation suggests.