I wasn't impressed.
So many of the characters serve no purpose except to die horribly.
And what was up with that stupidly convoluted plot to get her pregnant with the alien squid?
He gets some of the goo, then puts it into the guy's cup so he drinks it and gets infected, then he has to shag his girlfriend to get her infected so it can grow? I mean, bloody hell! That's hardly a reliable plan of action!
And as others have said, the fact that she can perform major surgery on herself and then go running around is completely unbelievable. Even if she was doped up on painkillers (in which case, why did she keep a clear head?) all that physical activity should have popped her wound open and spilled her guts out onto the deck.
And what was the point in Theron's character making it off the ship only to die under the collapsing SJ ship?
Also, the lack of subtlety regarding Chekhov's gun is appalling. The instant they said that Theron's quarters were a life pod, I knew that it would be used as such. Just make it a bloody shuttlecraft and it would work better. Show a bay full of the things, and then have one fall out of the ship as it takes off to crash into the SJ horseshoe.
And get rid of that bloody squid in her belly too. Just have the infant squid be the thing inside the canister, and then you can do away with the flawed chain of events that was in the movie.
A terrible disappointment.
I would agree with all of the above. The multiple agendas aren't juggled well, giving the whole thing a vague, convoluted feel. That's such a disappointment, because the hallmark of both Alien and Aliens is a relentless linearity that retains structural depth.
Overall, your specific complaints, though quite valid, are just symptoms of the main problem. The script simply hadn't been ironed out into a final coherent form. It felt like they started shooting with draft material.
Some lovely visuals, as always with Scott, but the whole is less than the parts.