FOr all its flaws, i too enjoy Prometheus. Beyond the characters questionable actions, the only thing that bothered me was the depiction of the engineers.
I am not a fan of linking them to human creation nor am i a fan of them being humanoid. For me, it takes away the very thing that made the Aliens Alien.
I would really like to read Aliens Apocalypse: Destroying Angels too. heard good things about it. ALso need to finally get around to reading ALiens Nightmare asylum/Earth War as well.