For me....My gripe was not the themes it attempted to take on. For me, Prometheus failed because it asked the audience/fan base to explain plot holes rather than simply tighten up the story before shooting began.
On the Alien boards, you've got defenders as well as naysayers all trying to explore the problems of the movie. Take for instance the two science officers who get lost. Yet, the ship has the entire complex completely mapped out. Surely the captain should've spent some time guiding the biologist and geologist back to a safe spot. Lets not even get started on the fact that the story sees the expert on rocks...the geologist get lost. Very sloppy. These are just a few tidbits a script doctor would've identified and ironed out.
As for those saying Shaw was a bad scientist. Into this I think she has an agenda. I think she has also been compromised by this. And, it gets the better of her. As does witnessing her lover burnt to death, being drugged, attacked by the crew and of course becoming a mother to a very nasty offspring. She emerges, to me, as a very interesting character that becomes difficult to swallow. She doesn't alert Vickers about the alien on board which is odd considering strict quarantine rules. But then again, why would she - she's drugged, clinging onto memories of her parents and figures if Vickers is prepared to scorch her boyfriend then she might be signing her own death warrant by calling the alarm.
But you see, I am filling-in. Its a sign of a bad movie when the audience have to do this. Filling in the gaps.