Let's see what you all think!

OK, so if I were writing this stuff, with Prometheus as my guideline as the origin, here's what my explanations for things would be.

Elizabeth Shaw had intercourse with an infected Holloway. He inadvertently passed along some of his infection to her. The Trilobite that she later removed was a product of her reproductive system being manipulated by the black goo, causing the normal egg/fetus to become that mess.

After escaping with David and re-attaching his head and bonding and having a jolly good time, David places her in hyper-sleep, knowing full well she is infected to a different degree than Holloway (Holloway ingested the substance, fully mutating his DNA on a circulatory system level, Shaw's exposure was through intercourse, altering her at a slower/different rate?)

He kills the Engineers out of spite, because he had indeed fallen in love with Shaw, proceeds to have the ship crash onto the planet. The "goo bomb" that decimated the Engineers goes airborne, infecting the planet and changing the flora and fauna. David, being able to read their language, discovers their history, their experiments, and their culture. He discovers that the Engineers were on a path to create something of a perfect design, one of which he discovers requires beings that resemble humanity in order to create (the mural from Prometheus explained). He leaves Shaw asleep because he knows her, she would be angry at him for destroying them before she could get her answers.

Now knowing that the Engineers created humanity and then wishing to destroy them for reasons unclear (they possibly felt that their creations would one day want to rise up against their makers?), David fully understands humanity's distaste for himself and synthetics (same thing, humanity made them, may one day wish to destroy them for fear of synthetics replacing humans).

He proceeds to manipulate the goo to his own desires, playing a sort of God because if the Engineers creations (humanity) can create things (himself and all synthetics), what could he create? He uses the parasite laying wasp as a starter. He then moves on to the plant life. Then he remember's good old Elizabeth, with a mini goo factory already working inside of her, still asleep. He brings her out of hyper-sleep, lies to her that the Engineers are all dead, she discovers he is lying, sends the "John Denver" distress call, then he incapacitates her.

He then experiments using her reproductive system, mutating her eggs into the larger Ovomorphs we end up seeing (makes sense if you think about it. Human eggs are produced in ovaries, inside those eggs is the genetic material that becomes a fetus. Ovomorphs house facehuggers or possibly trilobites?) She is in essence, the first "queen". 

The process is too much for her frail human body, and she succumbs to the experimentation's. David performs an autopsy, learns of how the goo works deep within a human host. He then realizes he needs more human hosts to continue what the Engineers left off on...the perfect organism. To his luck, he'll be able to continue on with it in around 10 years or so.....

Sci-fi fans, what do you think!?