"They created us and left clues for how to find them, with the intention of wiping us out if we ever did manage to find them. They were happy with their creations so long as we remained primitive and posed no threat. However, they knew there might be a time when we were advanced enough to pose a threat. That's when Plan B --releasing some variation of the xenos-- would come into play. Somewhere along the way, a whole bunch of them die for whatever reason. Humans eventually show up, wake a sleeping "sentry" and start demanding answers. He then tries to put Plan B into effect."
I like this reading. But...
"It's typical Lindelof. Being obtuse and mysterious just for the sake of it. And then providing no answers."
Apparently he's said that the "event" 2000 years ago that pissed off the the engineers and created the "spill" that killed them...is THAT THING that happened 2000 years ago. That's why all the crosses and shit (coz y'know fuck all eastern religions). Standard Jealous Gods stuff from his PoV.
Scott covers the religious themes. Gives a bit more room for interesting/less reductive interpretation.
I liked it but it bears all the hallmarks of something that was felt out on the fly/in production rather than structured. Hence all the characters having strange levels of development that don't quite play out equally to their individual importance.
I think the insta-rot Mega-Hugger covers that. The "weapon" lives to fuck, then dies when it succeeds - it's progeny is then born...to fuck.