Too much focus on the "they want to wipe us out" storyline. The film itself I feel contradicts every theory I've heard.
Why create us, leave a map for us to go to some planets only for us to find a military base? Absolutely no point if they were just trying to harvest us or whatever.
Why does that base have ships that want to travel to earth approximately 2000 years ago? Why are they breeding what look like WMDs?
I bet it's just a haphazard mish mash of storylines that are trying to be clever but just don't quite fit together as masterfully as we want and in a way that's what keeps us talking about it for so long. Pisses me off tbh.
The only one that fits unfortunately is the original premise of revenge for crucifying Space Jesus, which is enough to render the whole film absurd for me.
They should never have stumbled into the area of the origin of man. It just unnecessarily complicated an already hard to swallow and unoriginal Ancient Aliens angle. The themes in the film, God vs. its creation, religion vs. science, done in the most literal and hamfisted ways possible. Shrouded in mystery purely to hide the gaping holes in it and the leaps of logic required to maintain it. Alluding to a depth that really isn't there.
That need for mystery to hide the weaknesses in the story extending to everything else in the film, from the way characters behave to the lack of clarity in their motives. It's basically all thrown back on the audience to fill in the gaps to their satisfaction because the story that they are attempting to tell isn't a satisfying one in the first place.