Now why a race of ancient god-like aliens would have so much interest in terraforming a planet then engineering a race in their image (one you would guess would be planned to be subservient to them and less technologically adept), watching over them and manufacturing their evolution over billions of years? The time-scale is the main thing that bothers me.It may be that the race that terraformed Earth did not intend to wait at all, but merely moved on. They may have gone dormant (I think you suggested this earlier) like the race in Dan O'Bannons origin story for Alien. The clue, whatever it is, may not have been intentional, so when the precocious humans get in their FTL star ship and land on the alien world they awaken them. Elizabeth Shaw is described as a woman of faith and a little naive, and it may be that she champions the missions, only to discover that her gods are monsters, quite literally.
Further to the awakening idea, I have long thought that (based on the leaked SDCC images and the trailer) that the Jockey chair is actually activated by one of the crew.
Just a guess of course, but I like the idea of a dormant ancient race being awoken, but rather than being benevolent they turn out to be down-right 'nasty'.
The engineers sound like intergalctic chavs, smashing up bus stops, creating murals and starting the human race!