I'm late to the party but here goes.

This film was a trainwreck, but only a minor one (injuries but no deaths). Some random thoughts:

stupidest...scientists...ever
related to the above point; I was always asking myself "why the hell would you do/say/think that?" for almost everything the characters did/said/thought
you would think these folk would be a little more excited about discovering an alien species
what was with the cheesy looking flamethrower and tazer weapons?
did we have to have another android with ulterior motives?
Shaw and Vickers should have been combined into one character
no Charlize Theron in tight panties. Disappointing
did Scott intentionally make a film that had just enough Alien references to piss off the fans?
I liked the initial scenes with David before the others come out of hypersleep
the last 15 minutes are absolutely terrible
Noomi Rapace has an incredibly wide head
Scott seemed to ignore the Alien lore that followed his original film; he had the concept that the creatures were deliberately engineered weapons, but the introduction of the Alien Queen seemed to imply that they were simply a very dangerous and malevolent species
special effects still looked overly clean and tidy to me
it reused some ideas from early Alien scripts the same way TPM used ideas from early Star Wars scripts; the ideas were not used in the original films because they were stupid
I hated the ending narration; it felt absolutely out of place
Scott or the studio obviously felt the story was too weak to stand on it's own (read: make money), hence the massive amounts of Alien stuff retained from earlier script drafts and the advertising campaign that left little doubt to any fan that it was a prequel