If it wasn't an Alien movie by Ridley Scott, I would probably be less disappointed, but it was and I am. Not in the visuals, but primarily the script - almost certainly Damon "Lost" Lindelof's fault (although Ridley and the Producers should have demanded better of Lindelof and co-writer Jon Spaihts).
MAJOR SPOILERS BELOW!!
The beginning of the film starts promisingly epic and the Engineers look cool - but if their DNA was identical to ours, why do they look so different to average humans with huge muscular bodies, black eyes and albino skin? If they are unusual specimens of their species, then why are they so similar to each other they could be clones? OK, maybe different planetary and solar conditions caused the differences, but that doesn't explain how the Engineer gets out of the crashing ship at the end of the movie to attack Shaw without a helmet in the toxic atmosphere. It wouldn't be a plot problem except that the script makes it one by stressing their DNA is exactly human, rather than significantly similar. Bad writing.
A team of presumably top trained scientists and crew on a trillion dollar multiyear cryosleep mission don't know anything about the mission until they arrive, and only then is the reason for the expedition explained. Would have been solved by putting this scene earlier in the script, but here it makes no sense. Bad script editing/structure.
They find the alien site almost instantly - no surveys from space needed to find a small location on a whole planet despite not having a beacon to home in on like in Alien. Sure they might have done that without showing us in the movie, but then an excited Holloway makes it clear they found it by chance. Contradictory information - bad writing. Internal consistency required for successful suspension of disbelief.
One of the great things about Alien was that the crew didn't just land like it was a holiday jet landing on a tarmac strip - they knew landing on any unsurveyed planet was dangerous, so they did it with some trepidation. You know, checking if the surface is strong enough to take the weight of your massive starship? Again it wouldn't necessarily be a problem (it's a movie right?) except that Ridley so strongly established that genre realism in Alien. Literally a couple of lines of dialogue would have taken care of this.
None of them gives a crap about anti-contamination procedures, starting with Holloway who can't wait to breathe in potentially lethal alien bugs which haven't been ruled out at that point, despite the air composition being breathable in the structure.
Again a single line of dialogue about no bacteria/viruses/funguses being detected would have been faithful to realism, and mitigated disbelief. Maybe we could believe one character would be this gungho, but then others follow suit! If the others, apart from the believable Shaw, had instead reacted by shunning him or being suspiciously watchful of him from then on, this stupid action may have had dramatic impact, but no it's barely mentioned again. Stupid illogical character actions. Acceptable in a teen slasher flick maybe, but not what was hoped for here.
The cowardly geologist who loves only rocks, doesn't actually examine a single rock, let alone do or say anything a geologist might. In fact his first dialogue suggests some sort of badass mercenary type. He does the mapping, but all map data (kind of useful when exploring) is only downloaded remotely to the ship rather than also to a local mapping device he surely would carry? He then gets lost, and doesn't call up the captain who has the map and markers for the crew glowing in front of him for directions? Stupid illogical inconsistent character.
The biologist sees no danger playing with a completely unknown, potentially aggressive alien cobra creature, and doesn't spot or seem interested in the little worms earlier on, or in examining the 2000 year old alien corpses they found who died of unknown causes? Stupid illogical inconsistent character.
David may have studied ancient languages and be able to extrapolate to understand the Engineer heiroglyphs, but to be so instantly fluent that he has no trouble operating all the Engineer door controls and so on? Even so, when he starts endangering the crew by pressing every available button, no one apart from Shaw seems alarmed by his childish enthusiasm. Certainly no one backs Shaw up to rein him in. Hmmm.
What is David's motive in infecting Holloway - curiosity? Surely an alien pathogen spreading easily by touch in a drink, or a rampaging alien infected crew member, or alien baby are endangering his beloved Weyland? Or is he just evil?
Alien birth by robot caesarian - cool idea but almost completely undeveloped. Best body horror moment in the film, but imagine if it had been postponed for believable medical reasons right to the end instead, with realistic physical disability after such a major operation? Shaw prevailing against superhuman Engineer in those conditions could have been amazing and suspenseful. It would also have allowed her to still run about doing all the physical stuff earlier on without anyone wondering why the staples weren't being burst.
In Alien, we just about bought the idea of facehugger turning into huge xenomorph in a very short time, because we could think maybe it raided food supplies or something. How the hell did small alien baby turn into giant kraken creature in an operating theatre - not typically known for their extensive catering facilities.
What was the point of Charlize Theron's character? Yes, she's hot, but she's a great actress wasted here. The last minute throwaway father-daughter relationship with Weyland went nowhere - one of several intriguing ideas presented but left hanging (I'm looking at you Lindelof!). If Vickers was jealous of David, she hid it completely until the reveal of Weyland. Then suddenly it all gets Shakespearean? If there'd been some unexplained Vickers/David animosity throughout the earlier scenes, the payoff might have had some emotional weight.
And how come no one apart from Shaw, and Weyland's obvious accomplices, seems surprised to find Weyland stowed away on their ship?
The two co-pilots are barely introduced, except that they have some half-arsed banter and a disposable bet, then suddenly they are heroically sacrificing their lives at the end to save humanity, because the captain can't competently steer it enough for a ramming course. We don't give a crap when these secondary characters die either.
Why are there 17 crew members, but we're never introduced even perfunctorily to about 7 of them, who appear and then die. Their deaths barely register. There's at least one anonymous security type who leaves his weapons behind without objection on the first recce on the say so of scientist Shaw rather than obvious chain of command Meredith Vickers or Captain Janek. And well funded Company security don't have bigger weapons than ineffectual pistols when confronting alien infected contortionist acrobat zombies?
What are the Engineer holographs? Admittedly cool, but rather convenient. Some sort of alien captain's log? If so, why do they show just the bits that conveniently advance the plot - David doesn't have to spool or search through them at any point.
I'm going to stop now ...