Watch the EXTRAS and DELETED SCENES

Rating: 8/10 (15 June 2012)

There are still stupid parts to this movie-- i.e. running away from a rolling tire in a straight line, and these do not fix all of them, so much as to help to "grease the wheels" and ease the delivery of them.
I had to watch Prometheus twice to appreciate it. I wanted to choke Ridley Scott out the first time I saw it, but fell in love with it the second time when I watched it with no expectations.
You have to accept that these days, nobody will pay $160 million to make a movie that only a handful of hard core sci-fi buffs will go see and appreciate.
He made it clear this movie is only LOOSELY CONNECTED to Alien. It takes place in the same universe, but is its own genre, its own mood, its own story to tell. He may never connect the two story lines, the way Battle for Endor exists in the same universe as Star Wars but does not intersect plotwise.
The DELETED SCENES and WEYLAND FILES fill in a lot of gaps:
============================ >>>>1) VICKERS IS AN ANDROID ==============
She was quick to please at the suggestion she was an android. In the deleted scenes, she has an extended conversation with Peter-- and talks about how she was once attracted to him and found respect in his face, but now...he's an old crone. The "father" comment was not a poor rendition of even poorer George Lucasism, rather, a below the belt jab at Peter. She was pointing out that he created her as a plaything, but is actually a pedophile as he is technically her father.
Ridley likes to toy with the concept of androids having immature emotional responses due to a lack of a past set of memories. Her jealousy of David is also evidence, as Peter trusts him mo0re with intellectual matters.
======================= >>>>2) LV-426 vs LV-223 =======================
In the WEYLAND FILES, Peter specifies in his notes that they are actually receiving a weak signal from nearby LV-426, but only David knows this as well.
From the start, he knows the real bio-weapons prize awaits on LV-426, while he is taking "the doctors" (whom he views as naive fools) to LV-223 to find some technology they can sink their hooks into to extend his life.
========================== >>>>3) THE GOO IS A WEAPON ==================
The goo is a mutagen that turns the victim into a parasite and brings about the Xeno-form.
If you watch the deleted scenes, the Engineers know about the Xenomorph-- besides the wall shrine of a xeno in the goo storage room, Fifield and Milton find a shedded xeno skin on the floor in the pyramid. Also, all the dead Engineers in the body pile had familiar "exploded from inside" apertures on them.
========== >>>>4) HOW DID THE SQUID GET SO BIG? ========================
This was a major problem for me. Not only how did it get bigger, but didn't anyone else notice a wriggling thing in the auto-doc?
In the extended Vickers/Peter scene, she mentions that if he goes down to the planet, he will die, and that he should hear "that thing squealing in the room next door".
They found Shaw's "baby" and were probably studying it, keeping it alive, and feeding it. Or it got loose and ate the people studying it.
Either way, Weyland's people knew about it and had it in their possession prior to us meeting it again later.
============================ >>>>5) RETARD PETTING SNAKES ==============
This one is not a justification, but it helped make Milton's foolhardy attempts at petting a worm seem less abrupt.
There was a deleted scene where he finds some of those little worm things in the soil and has an emotional upheaval over finding the first non-unicellular extra-terrestrial life.
These ones were stupid and docile, and allowed him to hold them in his hand and pet them. After being exposed to the goo, they changed a bit in their demeanor.
======================= >>>>RELAX ======================================
...And watch the movie again. You might find yourself liking it the second time around.
All the music that I love most now-- I hated when I first heard it. It was a good movie, but did not spell things out for the audience.
Also, I think 20th Century Fox had more to do with it than Ridley Scott. They pushed for PG-13 rating from the start, and if you watch the deleted scenes, it is clear they add more edge to the movie and it they tried to make it more kid-friendly.