Let me dissect all the bullshit in this movie bit by bit:
First off we have the Engineer sacrificing himself to create life. There is nothing inherently wrong with this sequence except for a major visual error, mainly that of a (hopefully not the same one later on) black goo disintegrating the Engineer in order to spread life. The problem is two fold in this sequence. The first is that of the black goo breaks down his body in a similar manner, not necessarily as explosive as seen with the head, as the other black goo later on This raises issues of what exactly is the black goo, something I will address later on as that is a clusterfuck in of itself. The second problem is why is he doing this? This isn't an issue in of itself as the writers are entitled to a few mysteries. This is problematic because of the later scenes with the Engineers, mainly that they wanted to kill us. So we now have a race that created us and then wanted to destroy us with no explanation on either side and an apparent switch in behavior. This leads into the second issue mainly that humans were given directions to a military installation. Think about that for a second. Why of all places, a military installation instead of some remote colony to establish contact(they obviously didn't want to give humans directions to their home planet in case we as a race turned out to be evil or warlike)? There are two different assumptions I can theorize based on this and both are inherently flawed. The first is that the directions were indeed a poorly thought of trap for the humans in that we would go to this installation, get infected, and ruin our own race. The problem with this is that any semi-intelligent crew would have been much more careful and intelligent about their handling of the ruins and no infection would have occurred. So they would basically be assuming that this species of interstellar travel would be extremely idiotic and careless. The other possibility is that it could have been as Shaw described, an invitation. They could have used that planet as a possible staging ground for diplomatic relations. The problem with this is that it is a military installation housed with our equivalent of chemical warfare. Now before someone states that it could have been a diplomatic meeting point before they decided to kill us, remember that they had the alien mural there as well as the 'side-exploding mural' so they had been developing these chemical weapons long before 2000 years ago when they decided to kill us. Then another issue with both theories is that there is an xenomorph mural, one that doesn't look so much like a warning but rather religious in nature. They key factor there is the head down pose of the xenomorph and the way it could possibly be referencing the crucifixion of Jesus. Also note that Davis with his magical ability to read and speak the language of the Engineers, even if they do share Sanskrit roots, does not, out loud anyway, read any sort of warning sign.
Going back to the narrative, the next horribly written sequence is the infodump aka the meeting on board the ship. Apparently we have the crew, of a 1 trillion dollar project, not being informed what the hell was going on before they left. They signed onto a multiyear voyage without knowing what was going on and Weyland decided to roll the dice with a crew who didn't know what was going on. This is incompetence on two levels and done solely for two reasons, the first being that of a big expository sequence and the second is to beat you over the fucking head, as the movie assumes you're an idiot, with certain themes such as unwavering, fundamentalist-level, belief. I won't go into the whole Christmas motif and Space Jesus thing because first it's not in the movie and second, it's amazingly idiotic and contradicts with the timeline in the movie anyway. Mainly being they were directing us to the military installation way before Jesus existed.
Now let's talk about the crew of the Prometheus. We have Janek, Holloway, Shaw, Vickers, Milburn, Fifield and David. I won't discuss the rest because they get essentially zero screentime and die without any fucks being given. Even among this core seven, there are inconsistent characterizations and the only two that really have any importance, or even an arc, are David and Shaw. Before I delve into those two, let me discuss the rest. I'll start with Holloway who in no way acts like a scientist. The first beyond idiotic thing he does is take off his helmet in the cave despite not knowing if there are pathogens or whether the atmosphere is consistent throughout the caves. The second is later on when he throws a pissy fit that the Engineers are dead. Apparently the idea itself of establishing that there is indeed intelligent alien life, one of the biggest discoveries in human history, is not enough for him. Then there is Vickers who acts like the soulless corporate puppet. There's something to be said when people are suggesting that she actually is an android, even though that evidence is horribly unsound and contradicts multiple things. Her character is only there for the big twist at the end involving her father and even then doesn't really serve a purpose. Janek, moreso than any other character, is the heart of the movie. He is the one cracking the jokes and making the self-sacrificial play when needed. Milburn's character was fine up until the crew found the dead Engineer body. He then breaks down and runs away despite being a biologist and discovering an entire new organism, something that changes again later when the plot demands it. Finally there is Fifield. Oh boy. He first establishes himself as some sort of mercenary who is only in this for the movie who then turns out to be an actual scientist despite his whole wolf-howling bit. At first he seems claustrophobic when he enters the caves as he hesitates for a second and you can see a look of anxiety on his face, this of course makes no fucking sense for a geologist. His character just seems to be angry and crazy in general with no backstory to him at all. In general, there is very little to the crew and little in to making them relatable except for Janek.
Now for the star two, and there are problems inherent with them. David's character is broken down as the movie progresses and Shaw's character is built up. David, as we first see, is exploring the ship and wandering about in general. Despite his robotic movements, he acts in a rather human behavior. We see him eat, play sports, watch television, and study. All traits that are assigned more to a human being rather than a robot. He even has curiosity as we see with him investigating Shaw's dreams. This later leads to one of the great faults of the movie, we don't know whether Weyland gave him the order to poison Holloway or if he did it on his own. The reason this is crucial is that we don't know whether he took the initiative, which would enforce the curiosity aspect of his personality, or just was following orders, in that he was just acting like any other robot. Irregardless the audience starts to see him becoming more inhuman as the movie progresses. We then have him getting his head ripped off and of course, there is no panic because he's a robot. Despite the fact that his 'life' might end there, he seems perfectly at peace with it. Until, as you can guess, the very end when he wants Shaw to save him. This is contradictory in that he is now showing a human response despite earlier scenes with a lack of an emotional response. Ridley, or Lidelof(whoever you care to blame), however then go back to his breakdown into a robot with the line by Shaw that he isn't anything more than a robot. The main character herself is driving this point home in another "smack-you-in-the-face-with-it" line. Now as for Shaw, she suffers from the issues of consequential response in the narrative so her characterization really suffers from this as well. The main thing with her being a fundamentalist and having faith in the Engineers is obviously gone at the end, with her literally killing her god. She doesn't exhibit much of an emotional response to many of the traumatizing events in the movie such as giving birth to a squid, her boyfriend's death, seeing the Prometheus explode, nearly being flattened to death, killing an Engineer, or even helping David at the end despite there being the suggestion that she knows he killed her boyfriend or atleast she knows he was involved to a certain extent. The only consistent thing about her is the extremity of her belief, to the point that she is willing to work with David despite the fact that he tried to kill her less than a couple of hours ago. This of course deosn't make her relatable at all. Why should the audience attach themselves to a character that has shown themselves to be damn near idiotic? That's a question the movie doesn't answer and stands in stark contrast with Alien.
So back to the narrative, and the many issues found within. The crew land on the planet and magically in less than 10 minutes, find the structures. It's a movie so I'll give them the benefit of time but it does hurt the idea of scale and exploration in the movie. Anyway the crew lands and take the vehicles. However before they do, they have an extremely, and I emphasize the word extremely, stupid sequence in which Shaw doesn't want weapons brought with them. She has no clue what is on this planet, it could be wild animals or any sort of environmental hazard, and doesn't want anything to protect herself with. So anyway they go inside the temple and in a very convenient bit of movie magic, they can breathe inside the temple itself. As to why they were possibly terraforming? My first assumption would be for the Engineers themselves however at the end we have the enraged Engineer come for Shaw without the ability of a suit so it implies he might be able to withstand the hostile outdoor environment. However let's just go with that being a technical error for the time being. So the air is breathable and Holloway and crew, as I already pointed, stupidly takes their helmets off. Also thank god for that security camera footage to help speed everything along. Whew. It recorded exactly what is needed for the plot to progress and is played at the exact right time. Although it apparently didn't record anyone coming out of that room and there wasn't any bodies in the room itself. Oops. Oh and let's not mention the stupidity of going into the room in which the outbreak possibly started from. Jumping now to the part where the geologist, I repeat the geologist, gets lost in the caves despite the rest of the crew easily able to get themselves out in a quick manner. The geologist who also is in radio contact with Prometheus. Then we have pickup scene by Janek created for the excuse for Fifield and Milburn to lose contact with the Prometheus. Now right after Janek scares the everlasting daylights out of them, they head back to the headroom where they find a cute, and by cute I mean creepy, little snake thing. Of course right after being scared, Milburn wants to play with the thing coming out of black goo. This is a perfect example of events seemingly being written independent of each other. So both end up dead in a rather violent manner, which of course nobody notices, as everybody was getting laid while Fifield and Milburn get laid out, or the computer itself records.
So we now come upon the issue of the black goo(excluding the opening bit). This really doesn't make any sense for the audience as we see a plethora of different effects for this and nobody bothers to explain this. At best I can theorize as to what caused this as the writers apparently didn't give a fuck. So the goo infects a person causing their body to break down in a rather rapid manner however if they infect another person via reproductive methods then this leads to xenomorphs. Since worms are hermaphroditic then we can assume the snake things we later saw are the offspring of the worms themselves. The problem is with Fifield is that he's dead when he falls into the black goo but apparently goes back as a super zombie. So the black goo can also revive people from the dead as long as their head doesn't explode. If the xenomorphs are the goal of the goo then this weapon should be considered a failure as the incubation period is way too rapid in order to possibly infect someone else. What would have happened if Holloway hadn't slept with Shaw that one single night? He would have died and boom no xenomorph. This could be explained away if the xenomorphs are some weird byproduct. Of course none of this is explained at all. The driving force of the movie isn't explained and is pretty much used as a plot device in order for stuff to happen.
Jumping forward to after Shaw's abortion, we see her stumble into Weyland. Nobody mentions her physical state or where the squid baby is. David doesn't ask and the people who trying to put her into stasis, don't even look at her. I would also like to mention how they didn't bother to chase her after she hit the both of them. So nobody asks about the abomination and she apparently doesn't even tell. Hell she doesn't even show much of an emotional response to the amazingly traumatic experience she just had. David even makes a joke about it but doesn't care enough about the outcome. She agrees to work with the people who just tried to have her killed without any qualms, another example of a scene which has an emotional disconnect with the prior scene, as curiosity trumps all. Oh and Weyland has a nice scene with Vickers where she openly blurts the most obvious thing in the movie, that he's her father. This is a great case of less is more and assumes the audience is too stupid to figure that out. The tone and direction of that line also makes it seem like that was supposed to be a twist, in which this was another horrible twist compounded on the whole Weyland being alive bit. David also has a nice chat with Shaw in which he states that he wants to kill his parents, a piece of foreshadowing or so I thought, however nothing comes of it except to give the whole bit about Shaw's father being dead. So Weyland being the evil atheist wants to cheat death as there is nothing, and ends up getting killed. So what was the purpose of his character again except to waste time? Was it to expand Vickers in a shallow and obvious sequence? It's not like David had much of a chance to do his powerplay or even attempted to do so.
Now we have the captain deciding to kamikaze the alien ship in order to stop it from reaching Earth. He already telegraphed this in a very obvious line prior so no surprise there. The real surprise was how cavalier he was about it and his copilots as well. Hands up everybody! He seriously makes a joke right before crashing his ship which ruins all tension and the seriousness of the moment. Why should we take his actions seriously if he didn't take it seriously himself? Next comes the big rolling ball of doom or spaceship in this case. We have Vickers and Shaw trying to outrun it and all they needed to do was run diagonally. What makes this worse is how easily Shaw avoids this by just rolling, that's it, sideways. I can understand if she had to slid under something or run a moderate distance sideways to avoid the ship but she just rolls a little bit.
Next we have the squid thing all grown up and enormous in a matter of hours. The speed is pretty incredulous and obviously done for the sole sequence dealing with the Engineer, even though it could have been handled in a different and probably better manner. David then warns Shaw of the Engineer coming and instead of a lengthy stalking sequence filled with tension, Shaw opens up the door and the two monsters fight each other. A possibly fantastic scene cut extremely short. Shaw then leaves some cryptic ass message and goes off with David in search of more adventure. As to who played the flute? Let's wait till the sequel.
In short; the characters are inconsistent, the narrative is inconsistent and the lore is inconsistent.
And then Shaw thinks it's dead, and it's in a seperate module, one easily ejected from the ship if need be. And she's doped up on meds. 
