So I've just finished the game (for the most part. I've gotten through endings A through E) and am trying to piece everything together about the entire plot, the various motives, and how this relates to the Nier universe. Also read a few other theories that others had. Still a little confused. Here is what I think is going on. Curious to see what others think.
I think the overall plan of the androids (current cycle called YoRHa) is separate from Project Gestalt. I think humans had simply programmed the androids to destroy the machines and retake the earth while the aliens had programmed the machines to destroy the androids and claim the earth, plain and simple. The plan here is just to retake the earth. The fate of humanity seems to be a seperate issue. The pods oversee the human plan while that red-dress virtual machine girl oversees the alien plan. Ironically, both the original creators of said plans, humans and aliens, are both extinct.
Both sides (aliens and humans) understood the importance of continual improvement and incorporated evolution to their long term plans. The machines are evolving (machines learning and using different tactics, adam and eve, etc) and the androids are improving with each generation of models. This has gone on and on until our ending here with the red-dress virtual machine girl/adam/eve and pods gaining sentience. They've now decided that all this fighting is pointless (which it is) and thus the cycle has been broken. (presumably broken. the pods do state that there is a possibility for the cycle to continue. However, I think that this is highly unlikely since both overseers are now sentient and the androids 2b, 9s, and a2 know of the secrets about what is going on.)
I think Project YoRHa is just the name of the current cycle of the many cycles that have happened in the evolution of the androids. I don't think the entire plan of retaking the earth/destroying machines with androids is called YoRHa because the pods at the end mention that project YoRHa is complete. However, the note that 9S finds confirms that there is definitely a cycle of androids with each generation being better than the last and each generation using analysis of the previous generation's combat data. (note with title of "Regarding the Disposal of the YoRHa squadron") So we've reached the end of a cycle and YoRHa is considered complete. This leads me to believe that Project YoRHa is just the name for this current cycle. The previous cycles probably were named Project Whatever and there were also notes about the "Disposal of the Whatever squadron".
What do you guys think?