As others have mentioned, why did Holloway pretty much commit suicide? He had no idea what was wrong with him, he could have had flu for all he knew, and the motivation for David infecting him was never made clear. If it was a test then David was pretty damn poor at keeping an eye on his subject and investigating the results. Also, Vickers demise was so daft I almost shouted at the cinema screen. She goes through all the shenanigans on escaping the Prometheus in a pod only to get crush by a rolling ship because she's too stupid to run at 90 degrees to it? Come on, that's just stupid.
Also, no motivation nor explanation was given for Fifield coming back to the ship after whatever the hell it was that happened happened to him. I realise films shouldn't spell everything out for you but this left just too many blanks. The starting sequence was never explained and only made sense if you'd read what it was about on the internet, the procedures the exploration crew followed were unrealistic in the extreme, they landed and almost immediately jumped out and rode off to explore, very little in the way of preliminary investigation etc. They've just spent a trillion dollars and years getting there and they can't wait a few hours and be a little cautious?
Also, who was driving the lead vehicle in the convoy when the storm was approaching? If the storm was so dangerous why was Prometheus not damaged nor Shaws/Davids/Holloways suits show any sign of damage at all?!
I strongly suspect the end sequence with the xenomorph-like thing was purely put in to appease Alien fans and i think it was totally unneeded. the presence of Weyland on Prometheus was also not used to its full extent, having such a major plot development just lead to him getting cuffed on the head by an Engineer 10 minutes later and that's it was such a wasted opportunity. Plus Vickers being his daughter could be seen coming a mile off.
The whole thing stinks of AVP to me, alot of plot similarities (Influence of other species on Earth, alien Pyramids, a dying benefactor financing and accompanying the expedition), alot of cheap, poor actors used as extras we are supposed to care about with little to no character development. Instant changes in character motivations and no explanations as to why, If i had been told Paul WS Anderson had directed this I would believe you. Clangers in the script such as Fifields 'I don't care about you, I'm just here for the money' were cringeworthy, almost as bad as the bit in AVP where the scots guy in the helicopter gets out a picture of his kids, pretty much saying to the audience 'please like me through this obvious and lame attempt at character background because we all know I'm gonna die later'.
Prometheus had a whole damn planet to choose where to land, and they conveniently come down within visual range of what they were looking for? Gimme a break.
The engineer gets woken up (Why was it in stasis anyway?! How did that help it avoid the never-explained catastrophe that befell the others?) and decides to continue with the millenia old mission to destroy life on Earth. If it was that important a mission why was it not done by somebody else? Was it indeed going to destroy Earth? Shaw just makes that assumption with little to no evidence to hand.
The aforementioned unnamed crisis that killed off all of the Space Jockeys/Engineers must have been pretty major for there to be multiple ships present on the planet and all of them left alone for so long. If humans could land and explore relatively safely for a length of time why did the Engineers not come in an tidy up themselves?
The Engineers ship is controlled by boiled eggs and a flute. Hilarious.
The 'adult' version of Shaw's 'baby' is just left unattended to grow. Seriously, it's just ignored totally. It also looks like a bad Men In Black reject, classic Giger this aint.
Two scientists are left alone in the 'Temple/Pyramid' after presumably getting lost (this isn't explained and is made all the more laughable being that Fifield was the guy responsible for mapping the place!) and after encountering myriad dead bodies and spooky goings on they come across a strange alien snake. So they touch it. Yeah, that makes sense.
Also, not so much a plot problem but an intriguing question - What exactly did David say to the Engineer? Did he intentionally make it angry in order to fulfill a secret motive of his? Did he want his 'parents dead'? Hmmm...
I am also EXTREMELY miffed at the sheer amount of the film, including major plot points, shown in the trailers. Hardly any of that film held any surprise for me whatsoever, from Shaw 'giving birth', to the appearance of the Engineers, to the Prometheus being destroyed and the Engineer ship crashing. Poor show.
Compared to Alien this is a joke.