I am not really surprised...I think people wanted this movie to answer every question they had...which it was never meant to do. Plus, the questions it did answer they hate because it answered them in ways that contradict the theories they have in their mind that have lingered for 30 years. Plot holes are just a convenient excuse, every movie has them. Even Alien has them. (especially the original cut) The Alien diehards were going to have issues because this movie isnt the lead in they wanted. (it is exactly what Ridley Scott said it was, the father of the Alien universe) Let the haters hate they werent going to be happy unless they saw the Space Jockey flying the ship and landing on LV-426 and getting his chest ripped open with a Queen xenomorph jumping out to say hello. This movie was never supposed to be that Scott said it from day 1.
Interesting that rumors seem to be flying around that it is possible they may already have quite a bit of work done on the sequel (which is why it was talked about even before the reviews came in) as some feel they filmed both movies at the same time. (like Superman I and II were before Donner was canned and II was changed) There is no evidence that I could find (minus some talk about how long the filming schedule was in comparison to how much was shown...etc.) but since the Weyland-Yutani web site that was shown at the end of the credits hints at something big happening on 10/11/12 some are thinking that they will announce the Blu-Ray release and possibly have a teaser trailer ready. If true, Prometheus II will be the movie the haters want as it will be Shaw and David going to the Engineer Homeworld where they will most likely find out the true origin of the Xenomorph (which appears to have been alive previous to Prometheus as seen in the the mural in some form and turned into a biological weapon by the Engineers) and then the Space Jockey leaving while impregnated and landing on LV-426 waiting for Nostromo. Like I said it is a rumor, but seeing as they have never confirmed the budget for the film that could be the reason.