David is introduced in the third scene in the film, and then there's an incredibly detailed sequence depicting his routine. Just from that scene, we know more about David than we do about any other character in the film. We learn how he feels about humanity, about his situation, about the mission he is on. It's an incredible characterization infodump which is clever and subtle enough not to feel like an infodump. Actually, a lot of scenes in the film, even later on, are shot from David's perspective and clearly focus on his emotions and reactions over those of other characters.
The reason I think this is less obvious once the crew wakes up, is that everyone treats David like garbage. People ignore him. They refuse to use his name. They talk about him as if he isn't there. They try to remind him that he isn't a real person and has no emotions when he is clearly displaying emotions. It would have been easy to make that cartoonish and really hammer home that all these people are awful, but it's really well done.
Look, I agree, but that doesn't make David the protagonist. The protagonist isn't defined by the level of how well a character is fleshed out, though you'd usually expect them to be.
Shaw narratively fills the place of protagonist in key ways. In terms of plot, she's part of the catalyst as to why the Prometheus goes where it does, since she and Charlie came to Weyland about the star markings. She's the one who has something approaching a character arc, or at least, a character affirmation - she starts out with her faith, and even after going through all she does, reaffirms her faith in front of David. She's likewise the one who gives the monologue at the end - parallels with Ripley aside, it's standard hero's journey stuff. She ends with the line "and I'm still searching for answers," which ties in the ending of the film with the start of it. Plus, other things, such as getting the 'boss fight' of the movie for instance, and the equivalent chestburster avoidance scene.
David, in contrast, does everything at the behest of Weyland. Again, I like David as a character (he's probably the best character of the film), but functionally and plotwise, he's more just along for the ride. It's in Covenant that he actually becomes the protagonist of sorts (more like an anti-hero, but semantics).
All the actual problems with Prometheus are also present in Covenant. We have this huge crew who we don't spend any time getting to know and who mostly serve as an expendable buffet. It still can't decide if it wants to be a smart movie or not, and ends up being stuck somewhere in between. The script clearly went through a lot of rewrites and it shows.
There's more creative gore and action, so I guess you could say it's a less boring film, but even then so much of it is just stuff we've seen before. The shower scene, for example, was meant to be scary but is comical because it's so cliche.
Covenant does share problems with Prometheus, but I'm far more forgiving to them.
You could make the argument that the crews of both films act like idiots, but the Prometheus crew is meant to be the best of the best, or at the least, people that Weyland could afford to pay (i.e. a lot). And these numbskulls get lost in a structure that they'd mapped, destroy a head that they found, and has Weyland have David experiment on ONE OF HIS OWN SCIENTISTS. In contrast, the crew of the Covenant, while professional, aren't the cream of the crop, or at least, we're not given any reason to believe that they are. And prior to landing on the Engineers' planet, they've already under mental stress, including the captain.
Concerning rewrites, yes, Covenant does reek of rewrites, or at least, there's solid indication that it was 'dumbed down' after Prometheus. But then, Prometheus squandered all its attempts of being deep and meaningful, so what am I missing here? Covenant isn't short of allusions either via David and Walter. But I've said it before and I'll say it here, a simple story told well is preferable to a complex story told poorly.
David is a completely different character, which is fine, but I feel like we needed to see the change.
I think the 'change' in David, such as it is, was well done.
Everything David does in Covenant has groundwork laid for it in Prometheus, even if that wasn't necessarily the intent. I generally saw David as being condescending towards those around him. He puts up with their shit, but is happy to experiment on Charlie. He serves Weyland, but there's no sense of there being any fondness. He tells Shaw that (paraphrased) "sometimes, you have to destroy to create," indicating a disinterest in the wider stakes that may or may not exist (confirmed to later exist). And him contacting Shaw at the end comes off as self serving.
So, cut to Covenant, and David's in the position of indulging his darker aspects. We know that on the route to the Engineer homeworld, he looked up their history on the ship, and I think it's implied that he developed similar antipathy towards the Engineers as he did towards humanity. Engineers create humans, humans create androids, both humans and Engineers are flawed, only David is frustrated by his own inability to create. He can only create monstrosities. He can play music, but can't compose it. He has love for Shaw, but in twisted form, and it's further reflected as to how he kisses Walter - without any kind of passion. The great irony of David is that he's arguably as flawed as his creators, since he creates the xenomorph, and, well, how does that go?
I don't know. I don't hate it. It's far better than Resurrection, but it never rises above just being mediocre for me. I feel like perhaps they had interesting ideas at some point, and then the studio came in and said "Oh no, people didn't like Prometheus. Add more things from alien. Do more alien stuff. The focus groups like alien stuff. Make the protagonist more like Ripley. The focus groups like Ripley. There should be a fight with a xenomorph involving machinery. The xenomorph should run around in corridors. Do more alien stuff!" The result has good things and people clearly worked hard on it, but doesn't feel like the product of any deep passion or creative vision.
So, again, I can't disagree with a lot of that, but again, see the good story told poorly vs. simple story told well paradigm. Even if Covenant was made by committee, I don't have any problem declaring that it's better than Prometheus.
The one thing I would question is the idea of Daniels being like Ripley. And while that may be true, one has to question about Shaw in this context. It actually occurred to me that every Alien film has had a female protagonist,* while every Predator film has had a male protagonist, so is Daniels copying Ripley, or is it staying true to form?
*Alien vs. Predator also continues this tradition with Lex. Requiem is too wretched of a film to even have anything resembling a protagonist, much less a character arc.
I don't think anyone was hugely excited to tell this story, I think Fox just wanted to keep the franchise spinning.
Prometheus and Covenant were more due to Ridley Scott than Fox, I think.
I'm sure the info is out there somewhere, but from what I've read, I recall Scott being put off in the direction the Alien series went after his film. He commented that the hanging question in the first film was where did the ship come from, who was the pilot, why was it carrying egs, etc. This is a question that none of the subsequent films bothered to address at all. And while you can point to the EU, the Xenopedia EU has never really synced up that well with the films. So, Prometheus and Covenant were Scott trying to address this mystery.
Now, whether you think it's a mystery that needed to be answered, or whether Scott trying to shift the focus from the xenomorph to androids were good moves is down to opinion, but I think Scott was genuinely passionate about Prometheus - arguably less so than Covenant, but Covenant does come a step closer to answering this question, and in unifying the eras of the franchise (there's only 20 years in-universe between Covenant and Alien). But I think the films owe more to Scott than Fox, which is a non-entity filmwise at this point anyway. What Disney does with the IP, if anything, remains to be seen. Scott wants a third prequel film, but greenlighting it is another matter.