Loved the movie. Wasn't at all hard to follow. The script wasn't perfect, not close even, but the movie was solid from beginning to end.
The movie made sense but it doesn't spoon feed you every little thing and hold your hand. Everything was there for you to see or hear, I admit some parts could be a bit thin or you could miss a detail if you weren't paying close attention, at least in my opinion. A lot of open ended questions and such but I think I would have been less satisfied if all questions were answered.
Really, again, in my opinion, the microcosm was David, his "thoughts and relationship with Weyland and the humans. I mean, just watch David...what he says, his tone, his questions and especially his body language. A lot of what the movie is about is through David....our creation.
There was apparently 30min of footage left on the cutting room floor that may be in the Blu-Ray release, when I left the theater I thought to myself that it could have been fleshed out in more places.