The biggest thing I wonder about myself is if anything about the Watchers will make it in. The refrences to them in NieR were just that and they had no bearing on the plot (except for maybe the Logic Virus.) But if anything was gonna stick in our minds beyond just "Hey it NieR!" It would be giant cannibalistic babies.

And connected to that, the Intoners. Thematically they work somewhat like the Primals do which would make them good bosses for us to fight, and fall into our job description as Scions.