I just got back from seeing it a second time. It was very interesting to watch it again, knowing all the theories and the complaints going in.
I still enjoyed it a second time around. And I'm still not bothered by all the nitpicks.
This was not a professional scientific expedition. It was a corporate mission and they didn't care at all about scientific method. The two lead scientists were crackpot alien astronaut theorists that nobody respected. The geologist was a pothead (I forgot that part, lol). The other two scientists signed onto a two year expedition without knowing what the hell it was about; clearly they were the dregs of their respective fields.
I like the Sumerian thing that was posited earlier. There were two alien groups, the gods and the angels. The Engineers are the angels. The gods were the shriveled old aliens seen in the opening deleted scene. The angels rebelled against the gods, using the black goo bioweapon to kill them, but of course it got out of control and wiped them out as well. Since the angels were forced to sacrifice themselves to create life on other worlds, they now wish to exterminate those planets and remake them into their own worlds to inhabit.