I first went Minutemen, then Brotherhood. I never really liked the Railroad because they seem like a bunch of hypocrites sometimes when it comes to what rights a Synth should have, and the Institute because while their intentions seemed good on paper, their methods were a bit questionable. But I genuinely felt bad during all of my play-throughs, because I hated just wiping an entire faction from the map. During my Minutemen play-through, I loved that I could remain friends with the Railroad and Brotherhood, but didn't want to destroy the Institute. They had so much potential for technology that could have made the world a much better place, but it was controlled by a few bad eggs. And there were some very kind and caring scientists and staff in their facility as well, so it felt a bit wrong it destroy their entire lives because their bosses were shitbags. I felt the same way during my Brotherhood play-through not only about the Institute, but the Railroad as well. Sure, they have their fair share of radicals, but they had a pure and good intentions the entire time. And to just wipe them out for an out-there belief system of Robots and ghouls having rights just like humans seemed questionable.