The BoS seem reasonable to me. Now I suspect (I haven't play the BoS ending yet) they are in it for power and caps. Just like everyone else. And I have no doubt the Institute has agents within their ranks (they have them everywhere else) - but having played through the Institute ending, the Institute needs to die.
Synths are not alive. They are machines. Built to replace humans. Which is just messed. I sympathize with the RR though. Not because of their mission, but because of the cool "people". What I don't get, is how a human could make the leap into saving machines? Machines who mimic people? What's next? Killing someone cause they burnt toast in my toaster?
This is reason I like Valentine so much. He's know he's a machine. But he's a machine dealing with human memories. And he knows it (no spoilers - lay his story).
The BoS have a point. I mean look around, we have messed everything up. Especially Vault-Tech. Building bomb shelters to save people which are really various social experiments. I mean why?
The more I thinking about it, the more I'm liking the BoS.