I don't want to spoil the movie for anyone who hasn't seen it yet, so I'm going to try spoiler tags. Just in case they don't work, beware: SPOILERS! Seriously, this entire list is basically one long spoiler fest. You have been warned.
It's a visual feast, breathtaking in scope and with a myriad special effects that blow the mind. Ultimately, though, i think it could well be appreciated in 2D without the annoyance of 3D glasses - eventually I simply stopped seeing the 3D and everything went flat. I'd have taken off the glasses if the screen wasn't blurred.
Mouse over the next few paragraphs, as I've written them in white to avoid spoilers.
1. I still don't understand why the Engineer at the beginning of the film killed himself, to essentially create life (or that's how we were supposed to see it, which was confusing because the DNA was degrading so how did it make us?). Not to mention why the ship in the beginning was so vastly different from the half-moon Engineer ships.
2. Okay, LV-224. No, I still don't think it was meant to be LV-426. It looks like a very different planet, and as I've said before, if that were the planet where Nostromo landed, there would still be human remains, parts of Prometheus, etc - so I really don't think this is meant to be the Alien prequel (and Ridley Scott has said it's not meant to be, either). It's just not feasible, when looking at the evidence, that this could possibly be LV-426 or the planet where the Xenomorphs originated.
3. I was a bit concerned about all the awesome technology they have on this ship. If this is set years before Ripley and the Space Jockey, then why would Nostromo, Sulaco and the other ships be so far behind in technology when they would have come years later and benefitted from all that superior technology? Like the surgical unit - they could have used that to remove the xenobaby from Kane instead of rudimentary human surgical techniques.
4. Speaking of the surgical bay, that was awesome. Damn, I was impressed by that scene! It was amazing. On the downside, what the hell? She somehow gets away from the other two doctors, makes it down the corridors while stopping every few metres in agony (and they can't catch up to her?), no ship-wide broadcast to tell people to watch out for her, gets into Vickers' personal quarters unopposed, uses the machine (still a great scene), then gets out and wanders around the ship half-naked and bloody, and no one says a damn thing about her condition when she runs into Weyland and David? And she doesn't feel the need to tell them what she took out of herself? And they're all okay with travelling back into the Engineer ship without ever discussing what the hell happened to her and why she looks like shit and keeps clutching at herself? Really?
5. I thought David was fantastic. Just freaking fabulous. Michael Fassbender rocks my world. He's a great actor. BUT, if he was some advanced form of android, then what the hell did they end up with when they got basic androids Kane and Bishop? Surely these should have been more advanced?
6. Also, Weyland says David is his only son. Vickers is his daughter. So what the hell? How did Weyland-Yutani get started? Or did some other offshoot of the family take over and build it into the Corporation? (On a sidenote: Bishop was created by Charles Bishop, who shows up in Alien 3. But in AvP, set years before Alien, there's a Charles Bishop Weyland. What, did the family tree diverge?)
7. I'm still confused as to the pile of dead Engineers. If they died due to the disease, okay. But they were chest-bursted. So where the hell are the things that came out of their chests?
8. The Engineers needed their space suits to walk around on LV-224, apparently. They could breathe in Earth's atmosphere - which is why the inside of their ship had breathable air - but needed suits elsewhere. So how in the hell did that Engineer make it from the alien ship to the crashed shuttle without his helmet? Could he just hold his breath that long?
9. The running. Always in a straight line under the massive fucking ship that's rolling down to crush them. WHAT THE FUCK. I thought these were super-smart people. RUN TO THE SIDE, MORON! Gah!
10. The xeonomorph at the end is not the Alien we have come to know and fear. Its face and teeth are too human, for one thing, and its skull is pointed and very different from the dome shape. Yet another reason I don't think this is the proper Alien prequel; that's not where the xenomorphs come from, at least not the ones that Ripley et al encounter. Also, Ridley Scott has said his prequel will have two parts, so chances are somewhere in there will be those two who blasted off in the other Engineer ship. It's entirely possible that one of the ships carrying the bio-agent had a spot of bother, ended up with a form of xenomorph roaming the ship, and crash-landed on LV-426, providing the weirdness of the Space Jockey being completely out of place.
11. What the hell happened to the biologist's body? (Which, hello, STUPID MAN, what the hell kind of biologist is he to try and pet an obviously aggressive alien creature? NUMBNUTS! He deserved what he got.) There was zombie-geologist, which was completely out of place and made no sense - just there for shooting and explosions and shit; but he wasn't infected, just killed. But biologist-dude was impregnated. So where is his body, and where's his alien? Ooh, SUSPENSE.
I loved, loved the Prometheus; one of the sexiest ships I've seen in a while (it's the space-pod engines; I think they remind me of Serenity. Serenity's big brother!). The cinematography was incredible, the world-building was amazing, I enjoyed the acting for the most part, and I liked the special effects. Still, there is something missing; I'm not completely satisfied. But I'd watch it again, and probably buy it for my collection.