Im one of like 3 people who actually liked Alien 3 and Resurrection though I won't dispute they were not as amazing as the first two.
Prometheus reminded me a lot of reading old scifi where it's not really about the characters, as much as it's about what the writer wanted to show us. The characters are there as a vehicle to make that happen. And people aren't very used to that, I think.
There were a lot of weird little "this doesn't make sense if you think about it", but you know..you just gotta live with that
edit:
A few things that stood out to me as "strange questions":
There's murals of the xenomorphs but they haven't been created yet. The movie later seems to follow that the goo creatures evolve towards that form, but were they intended to do so all along?
The android finds green goo while exploring. It's probably just a fan service moment to remind us of Aliens, but assuming there was indeed a xenomorph outbreak (or some other mutant critters)...it'd have happened 2000 years ago. Doubt it'll stay moist when they show up to explore.
A lot of bad horror movie character decisions of course (getting lost in a cave, while in radio contact with the guys that have a 3D map, petting alien snake beasts etc)
Why did one engineer stay behind in cryo freeze and how did he survive whatever killed the rest?
Sure, it's science-magic, but how did the alien squid grow to monster size, without anything around to eat and gain mass?
Probably thousands more
