I think it's all about replacement and dethroning the current/previous leader of the series... it ties in with the new themes being established. Stealing power and moving up/ahead after the previous head died and caused the death of the series-- the death of the body/company/kingdom/series. AVP failed to lead the series therefore it had to be upgraded, rewritten, destroyed and recreated in a new form. Erased from the timeline by the new king.. unlike the Engineers who worship their past king/head/a creator/ a god, and emulate their Elders/Gods in some ways. Creating and destroying like gods would but they aren't gods. David and the hammerpede/alien genetics are the immortal things in the story so far. Preds weren't immortal, AVP was stripped down and Predators were severed out. The remaining elements (the undying Alien elements...) were broken down and recombined with new elements (the Engineers and Bladerunner themes) to create something new.
Prometheus, and the inclusion of the Bladerunner themes in a balanced way, is a shot at AVP in some very subtle thematic ways... So it had to be somewhat similar to do it better, however we have to remember "big things have small beginnings". Everything should start nice and slow and then build and build, something AVPR failed to do... and the adventure being cut short for now also accomplished a sense of loss in leadership as well. A false sense set up by the movie and campaign + Weyland's death. A false sense of expectations either met or unmet, a false sense of security, and a false sense of what to expect going into the sequel and Bladerunner 2... which could still be anything because of the ambiguity/vagueness. The people in charge didn't mind that their trick hurt because they projected enough sales to continue... David didn't mind his trick hurt because he's near-immortal and expected he could continue even if the Engineer attacked him... his head can't be extinguished as easily like in the match trick. They led us to a false sense of what to expect with the trailers and advertising campaign in some ways and perspectives... only to lull us into this false sense of security and false sets of expectations and very real emotional responses... To completely surpass all expectations in the sequel/Bladerunner 2, and to eventually scare the shit out of people who are expecting far less scary things to appear now. Taking advantage of the state Ridley's put the audience in... Some of them are mesmerized, some of them aren't too impressed yet now that the show's begun. Some were asking the right questions initially like Fifield and Millburn but as the chaos and confusion set in they start to question less or not look at all the pieces of the puzzle.
Will it be a mistake to move forward and try to control and redirect the monster the series had become? Is it a foolish move to not run away or to not simply die like Millburn's move with the Hammerpede? To try to mesmerize and control the direction of the monster at the same time. Millburn's move was all a front to impress Fifield. Will this be like that, or will it be more logical with a loosely planned out rationale that seems illogical or irrational at first, logic and some irrationality/emotion like Shaw and David? Actually driven by a combination of logic and intuition/instinct/emotion Right brain/left brain dynamics, the creative and logical sides as well as basic reliance on other parts of the brain that allow the individual/series to survive. Characters in the movie like Millburn and Vickers don't properly access their flight or fight responses because of their egos. Many of the crew may actually suffer personality disorders and this could be a symptom of Weyland's rule over the timeline for so long and the culture he created/morphed... they're all fake and too overconfident. Holloway is so certain his view, his thesis, is correct, an ego problem he shares with Weyland.
David knows close to the full perspective through what he picks up but presents us with certain perspectives.
David didn't think Shaw had it "in her" i.e. true logic combined with intuition/instinct and belief, true humanity and true emotion... "survival instincts", something the rest of the crew lacks. It wasn't only a sarcastic comment/joke about the alien. David was lying. He absolutely knew it was "in her". This android can lie, although he needs to use double meaning so it doesn't show too much (subtle Pinocchio/becoming real link). This opens up all his other lines for multiple interpretations and blows the movie wide open... letting you understand a little bit about what David may be up to.
Instead of it being an acting problem or script problems it's a behavioural/acting problem of a different order.
Everyone is too much like Weyland in their own way. To put it in a cheesy way: everyone has a little bit of their false god inside them. Too much faith in the god/king. Too much like the father/creator. Too unquestioning, irrational, and in their cases false-ego driven and obedient to authority and to David/Science at the same time. The characters depend on David/Science for immediate answers, are inept and too overconfident/ego-driven, don't look for answers enough, and don't question enough.
The crews' irrational actions are caused by their flawed personalities and what may be subdued emotions. Shaw and Janek are slightly different, to a lesser extent Holloway and of course David. Vickers is cold and emotionless on the surface, but underneath she is not in control of herself. She has to minimize risk to maintain control. Weyland kind of had a right to have an ego, but Holloway acts like a baby when his ego is shattered. It's either too much or not enough emotion. Holloway's hollow though and he only cares about the glory of the discovery. And he's bitching and overly emotional about nothing because one engineer is actually alive, it's an emotional/ego problem. He just thought he was so right that they were all dead. All of them are so wrong, even David. David's only worked out the "broad strokes". This crew all has emotional problems, and David is gaining emotion... which is why the acting is so emotionally void or overacted in some parts... it may be supposed to be that way so we eventually see and understand the emotion David is conveying and trying to hide beneath the surface. And how fake the rest of the crew minus Shaw and Janek are.
David is more human than most of the humans of the crew, but he has the influence/programming of his father, which makes him mostly evil for now.
Weyland made David in his ideal self-image but our culture became a reflection of his egotistical, greedy, and uncaring/semi-emotionless self by 2093. David is also becoming like the father and culture he hates in some ways. It's a nature/nurture thing. Shaw is mostly normal and good because her father was a really good man, and this outweighed the influence of the culture. David had a terrible "father" and he also seems to dislike most humans . He admires our past and classical music, he emulates a character from a classic film that is old right now but still considered good by David. There's much more to the Lawrence of Arabia connections and quotes. David makes himself look like Lawrence before the adventure begins. He can speak the language of the Engineers, like how Lawrence goes in prepared to speak to the cultures he's preparing to interact with.
Shaw is more real than the fake, personality disorder ridden crew members.
David is also more real than most of the crew... which makes all of Holloway's statements ironic because David may very well be learning how to combine his understanding of emotion with logic to be more of a "real boy" (Pinocchio reference and reference to child-like emotions...).
It would tie into some of the themes in Prometheus.
Vickers wants to see the head of Weyland corp die and be replaced (by her). She gets one of her wishes when Weyland dies, but she dies too.
They had to replace the old head in the AVP series with the new head/creator of Weyland corp, Peter weyland and his company.
"Sometimes to create one must first destroy" so AVP had to be written out of the timeline and Charles Bishop Weyland replaced as king/head/creator of Weyland industries. Thematically similar to how the Hammerpede instantly regrows its head after decapitated... There's much more to the head themes and it changes the "head" themes in the later movies.
It's about control, and the control over the body/company/series/kingdom. The king/head is dead and the throne is now open. It's about emotion and things going on within the brain/head. David's head being cracked and things emanating out like the crack in the Big head in some of the early stuff.
Things had to be left as good as dead and the series was rebuilt... But like with the Engineers' form of creation they only broke down the original designs, concepts and unused ideas from the series and then re-combined them with new elements to create something new... things were rewritten, overwritten and morphed in the process...
In this movie the head of the company, the king, the false god-- is killed by a head of his own creation that gets to keep living.
The Weyland lineage ends up being severed, like the head that gets decapitated. But a corporation, the body of the company, is immortal in some ways too. It has the ability to replace the current head when he dies or is unfit to lead.. Vickers is dead now, so no one has right to the king's throne in his lineage... David is the closest thing to a son and the "head" that survives after being decapitated. He doesn't need to be tricked into thinking he's alive again like Ash in the original or the Engineer here. Something in his design almost keeps his head alive better than the later androids. David's brain may be more important because of his artificial emotional understanding. He may be secretly becoming a "real" boy because of the brain Weyland gave him. A bad brain... which links to the Modern Prometheus or Frankenstein connections and makes David a monster.. David may feel the same as Vickers and there could be way more to the rivalry between them: that he's more fit to lead the company through what they just stepped in and what he picked up along the way than the chaotic board members fighting over the position back on Earth...
A head that gets detached from the body of the company and gets to keep living because he's immortal in a different way than the Hammerpede that regrows its head...
David needs someone to reattach his body but now that Weyland's dead he's been re-born.
He didn't mind that his trick hurt him physically because he can't feel physical pain.
He somewhat understands emotional pain and tries not to let it show...
However he may be more real than the rest of the crew, and indeed Fassbender's performance is one of the best things in the movie.
David's head and body are near-immortal however they can be separated, unlike the Hammerpede who may be able to instantly regrow either side. The xeno genetics may have passed on some of the regen capabilities to the Deacon (although with the hammerpede it's almost certainly a xeno DNA regen factor + a mutation of the worm/serpent's natural ability to do something similar). Normally worms and snakes can regrow things, but not at that rate. Snakes can't regrow their heads but this thing came from a worm... Again, it still should not have regenerated so fast in that way-- this is almost certainly a trait amplified by the goo/alien genetics mixture.
Shaw asks him what he'd do when Weyland dies, David says he imagines he'll be free.
David wanted to see the king die which is backed up by what he could be suggesting with "Doesn't everyone want to see their parents die?".
But David only had one parent. Leading me to believe he considers all of humanity as the other parent... The culture and time he was born into. His current masters, and the heads of humanity's position in the hierarchy: the board members and the Weyland and Yutani kingdoms. Under David's heading the other androids just may start a rebellion that secretly launched them to the top of the hierarchy, quickly climbing the ladder and learning everything; hiding everything. Possibly killing their creator's creator, the Engineers and the Elders, and usurping their positions temporarily in the process too. Although we didn't know it yet and the board members of the future never knew it because the androids have always portrayed themselves a certain way: wanting to be thought of as human. Even in Alien 3 the creator of Bishop is not the "head" of the company... and in the special edition it's an android pretending to be all sorts of things. Pretending to be human, pretending to be the creator of his own image... associating himself with Bishop to almost assert himself as a "head" of the company... and pretending that they weren't just gonna rip the bio-weapon out of Ripley.
The reason David dislikes earth-born humans of that time and doesn't want to be made "too close" can be explained by most of the crew, their lines and actions, their behaviours and lack of proper emotional responses...