The Charlize Theron character is a problem from the start.

ending scene is AvP like in it's sillyness.

In the final third of the film Peter Weyland is revealed to be alive, and in fact has been there the whole time. But I gained nothing from this reveal other than a 'um... that's interesting I guess' kind of response. A friend later told me that him being alive helps make sense of some of the bizarre actions that David was doing throughout the film, like using Logan Marshall-Green's character as a test subject to find a 'cure' to Weyland's impending death. But I didn't really get that, so for most of the film I saw David doing seemingly malicious things without a hint of malice, and ultimately came at the expense of any drama coming from an understand of why.

In my opinion, the film would have been much stronger if it was revealed at the beginning that he was alive, but remained a reclusive and shadowy figure in the background, dealing solely through David and Charlize Theron to deliver orders. Additionally there's nothing really gained from having it a big reveal that Charlize Theron is his daughter. If we had known that from the beginning, it would have made her a much more interesting and sympathetic character, someone who strives for her father's approval (putting up a facade of being tough and ruthless), but will always come in second to the always obedient David (who he sees as a son). This is all hinted at the film, but most dramatic impact is lost since it's revealed in the third act, by the time I stopped caring.