I havent don't the Institute ending yet; however the Institute is the most malevolent faction in the game. They keep claiming they have humanity at the heart of their goals, but there a lot of humanity on the surface whom they're a parasite to, and do everything to be isolated from. With just a fraction of their understanding and resources they could do a lot to better the Commonwealth.
They don't need to replace anyone with Synths to do their goals. That is an entirely selfish and more then likely evil action. I dont think we're ever told what happen to the kidnappee but they're more then likely dead and might just be reduced to their base components for raw materiels.
The Institute is out only for themselves.
---
Minuet Man is the most altrusic, but ultimately a band aid. They're a reactionary force, not a proactive force. Maybe if the Minuet Men can become a confederation of homesteads, maybe? But how they function for the last 100 years, is that they're a band aid.
---
Railroad isn't really worth discussing. They're not a faction that'll turn into anything more then what they are. Though PAM is largely a waste for them.
--
BoS is the best faction in the game. They aren't the most selfless faction but they're the most proactive group. They're gonna take out super mutants, raiders, and feral ghouls. They aren't taking them out because they want the farmers to live a more secure lives, thats just a benefit.
Thats why the BoS is the best faction for wasteland. They're a stabilizing force, which then promotes growth and security.