Here's what I'm hoping for:
3 Main Factions
1) The Institute - Android creators that are working to improve humanity's plight. They make the argument that android are not actually humans and that the research involved could aid humanity greatly.
2) The Railroad - Humans working to free the android that appeal to a person's emotions of compassion and freedom.
3) The BoS - They don't have a horse in the race when it comes to androids and will more or less do what you want as long as they get their hands on the Institute's tech in the end. They should convince you that they can put it to better use than the Institute with their vast network of chapters.
I guess technically 4 as the last option would be to not choose a side and take over the Institute for yourself.
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Basically, no distinct good or evil options. Each side has different motivations/advantages that appeal to different ways of thinking.