I've watched this twice now and have to say that I was surprised I enjoyed it so much.
I've decided to write my thoughts without rereading all the previous comments. I may repeat what others have said but I may also add new ingredients.
The filming is stunning, the sets great and the effects awesome.
I was already aware of the 'reality' issue of Dr Shaw running around after major surgery - so perhaps I was less 'shocked' when i saw it, i also thought I am watching a film about Aliens creating us, so perhaps suspending belief can accomodate this.
I felt that the film was similar to the original 'Alien' because it leaves more questions than answers, which I like (rather than the franchise sequels which seemed to focus on the singular visceral battle between humans and aliens).
I also like that it opens the field up to a range of possible presequel sequels - including following Dr Shaw's journey or further exploring the evolution of the 'Alien'.
I thought the film had more characters than the original but mostly less developed. I thought it was lazy to have the neurotic weedy mapper and the geeky biologist as the negative characters that die off first. At least the negative characters in the original also had 'heroic' moments as well.
I was surprised that the guy who maps the complex got lost......
There were a number of continuity flaws, including lots of flashing lights in the long shots during the storm rescue, but none in the close shots. also where did David get that solid looking ladder? the captain asked the 2 lost guys "where are you" when they were clearly indicated in the 3D map.
Similar to the original alien where the blood dissolves floors but but is staunched by a cotton wool swab, the helmet of the mapper is affected but nothing else touch by the copious spray is.
I thought the range of Alien lifeforms was interesting and again raised more questions than answers - the worms arising as soon as they stepped into the inner sanctum showed that it was not all in storage. The thing in the other doctors eye and the initial moving of the top of the vessel david looked at. I have read that these may indicate an evolution of the alien lifeform, but they seemed different and seperate to me, even if the procreation methods were similar for most.
The different effects of some alien life on human, why is that?
Why did the vase david picked up neither ooze nor have the top become less solid?
I thought the use of the huge deaths-head carving on the outside wall was unecessary - it was so big they would have seen it going in.
Why did the dead engineers head explode?
Why did shaw and the vickers run along the line of the falling spaceship when a sideways movement of very little would have been easier?
why would such a clever race of beings create a cache of extremely dangerous (even to themselves) living biological weapons to destroy humanity (and or others) when a mass delivery in aerosol form of the DNA breakdown liquid would be much safer?
The extras include a slightly different beginning a few extended or deleted scenes and the fight between Shaw and the last engineer was longer - it included a small part where the engineer saw the replay of the message sent that included the girl playing the violin. Although no sound you could see the engineer was understanding that the humans could play music, and this seemed to make a difference, like recognising a companion soul - until he tried to kill Shaw anyway.
I noted david called dr Shaw Lisbeth when complimenting her on getting the alien out of her stomache - a subtle reference to her earlier films....
My two penneth worth....