A few inconsistencies stick out in comparing Prometheus to Alien. They are supposed to exist in the same universe, so it's a fair comparison.
For example, why does the Xenomorph at the end emerge from the Engineer's body as a human-sized being, when we've previously seen chestbursters to hatch much smaller than that?
It's not so much about things being "unanswered" as it is them simply making one wonder why create these inconsistencies. They don't ruin the film at all for me, but they drag it down a bit.
Lindelof's fingerprints are all over this. I'm curious as to how he continues to receive high profile work. It's mostly due to his relationship with JJ Abrams. But the guy simply isn't a very good writer.
Another question - how exactly did all the Engineers die? We're led to believe that their "weapon" turned against them. That's presumably why we saw the holographic recordings of the Engineers running from something. But if we assume it was either hugely tentacled creatures or Xenomorphs, what happened to those beings?
Maybe I missed something there, but it's disappointing that the more I think about the movie the more I question. LOL, Lindelof.