A couple of things I want to throw out there, perhaps been discussed before:
Can we determine the possibility that the juggernaut ships, both the very bio-mechanical looking drop ship we come to know from Prometheus and Alien, and the new "mother juggernaut" we're seeing here, can these ships be the result of stolen technology?
The city looks like any other ancient civilisation city, with stone and structures; Rome comes to mind when looking at these pictures, especially given the religious nature of the Engineers. So, what if the ships are stolen technology? Maybe this fits in with the civil war aspect, as well as the difference in how these Engineers seem to look, and the suited/military appearance of the ones we saw in Prometheus. The technology doesn't seem to fit with what we're seeing with the city. I'd expected the home world to look a lot like the architecture of the juggernaut. Obviously not.
Perhaps, 2000 years has evolved (or devolved) the species to look more humanoid? Or, are we seeing just another colony of Engineers as part of a greater, more diverse civilisation, a defect of the civil war? Maybe these ships are leftovers from the war with another breed of Engineer. Maybe they're products of a different race entirely.
Ridley has really opened up so much possibility here. It'd be a shame if he wastes all of this new lore. I wanna know things, damn it.
EDIT: and if there's such a diversity, the Jockey might just be another remnant of the Engineers, something completely different from what we've seen. Bigger and more advanced. Or, we're just gonna have to accept the fact that Ridley wanted to change the size to fit in with this new approach. That's something that'll have to be overlooked, I suppose.