Prometheus turned out to be your stereotypical modern science fiction film. It was nothing short of that. It was a take on the birth of the Xenomorph breed.
The movie made little correlation to Ridley Scott's Alien.
Prometheus was the name of the ship and correlated with the god of the same name. It was about a birth of a new, greater breed. However, the plot holes leading up to "Alien" were evident quite a bit.
The opposing creature this time was an alien humanoid noted as nothing within the actual film, but dubbed "an evolved God-like version of humans". Noted as "The Engineers". This being stood as a pale, 8-foot, physically and intellectually advanced being that predates human history. He appeared in the opening scene being visibly ripped apart at the molecular level and being 'reborn' into this advanced being.
There was an example of how one of the crew's members became infected by a disease, a parasite, that infected the male and impregnated the otherwise sterile wife of said human male (of course, only after Hollywood-style implied sex). This child was nothing less than a starfish, an adaptation for the earliest evolution of our favorite "Facehugger" aliens.
Hopefully, Scott was peaking of making the film into it's own franchise with a sequel. This will create a feeling of spiritual succession for the full Alien franchise.
If this is true, this will explain the various plot holes in Prometheus. It will create a standalone series where our "Alien" beings merely exist and play a smaller part in the story as a whole. This could possibly bring up a variation of our "Predator" series as well. I suppose only time will tell.