I was pondering this for some time but it was only having one of those bad pizza dreams that it all came together. I wanted to discuss this but wasn't sure if this was already discussed somewhere else on the website.
Here goes, what if the SJ are actually modified humans, basically descendants of humans but taken in a different evolutionary path, that are super evolved and we didn't come from them. The selected were offspring taken off world as depicted on the pictograms, Kinda like a historical Alien abduction. The nephilim race comes to mind, yes it is mentioned here, but it's not really applied in context of the movie. The SJ seems like hybrid beings. A mix of two different humanoid species, perhaps one part human and the other half from a purebred off world heavenly humanoid specie.
They're are called engineers but the assumption is that they engineered humans, that might be misinformation and a smoke screen. One possible clue is the language in which the Engineer understands. That so far is the timeline when the two coexisted in some form wither mutual or not, only thing remaining that is similar between for communication is that ancient euro-indie language, whatever one calls it.
In the pictogram, those seem to me like Alien adductions and the engineers ran experiments depicted on the funky Geiger pyramid life cycle art. Earth was a testing and breeding ground. We see this in popular pop culture of alien abductions of people being probed, prodded and being experimented on but not in context to Prometheus. Perhaps it isn't like abductions to the humans and more like human sacrifices for worshiping their Gods, the SJ.
Wanted to throw this random word in the mix, Nihilism: A doctrine or belief that conditions and social organizations are so bad as to make destruction desirable for its own sake independent of any constructive program or possibility - A doctrine that denies any objective ground of truth and especially of moral truths.
Shaw's questions went from why did you create us to why do you want to destroy us.
I have not yet seen the uncut version, but will this week. Those that have seen it could this ideas be possible?