But Cerberus is just a tiny fraction of humanity, and then they are ultimately painted as the villains over the course of the series.
I'm talking the vast majority of the species; which in a refugee scenario not unlike the one ME:A is pointing to wouldn't be all that hard to do. I want to see something that involves the human colonists as a whole, not some minute fraction wholly unassociated with the majority. The destruction of an alien ship, later found out to holding civilians including children, because the majority of the human population did't trust it flying so close to our holdings. An attack on the colonists because our prospectors desecrated an alien burial site, etc. Something that can paint the entire population in a morally grey light.
I don't think BioWare will do that.
Hmm, I'm not sure this is a direction that would be followed either.
However, what you suggested sounds great to me. I'd like to see humanity enter that morally grey area that sort of hung around some of the other races in the trilogy, like the turians and salarians (genophage), krogan (rebellions, devastation of Tuchanka) and the quarians and geth. Humanity were free to be in that sort of judgmental seat, where they could sort out those respective problems, and be championed. I'd like to see a sort of reverse, where humanity be truly accountable for whatever morally questionable actions they may or may not commit in Andromeda.
And hey, BioWare has plenty of examples of humanity doing wrong in the real world to draw inspiration from, same goes for creating a human antagonist if thats what is going to happen.