I joined the Brotherhood first after meeting Danse. Fallout 3 was the only exposure I had to the Brotherhood prior to this game, and so I assumed that the Brotherhood was an institution dedicated to preserving technology and helping people survive the post-apocalypse. And that is still true, but I didn't realize how xenophobic the Brotherhood was, and after being asked to kill a certain scientist who had helped me previously, I felt very uneasy about remaining with them. This feeling was further exacerbated when I began to meet a lot of synths who were just... people. And in Valentine's case, very good people. People I would consider like myself. When synths became less sinister to me, it made the Brotherhoods position untenable. I ended up helping the Railroad, remaining undercover working for the Institute until the critical moment arrived where we could evacuate the rest of the synths. During the course of these events the Brotherhood attacked and we retaliated by destroying them.
I didn't really want to destroy the Brotherhood though. I just didn't agree with their position and their fanatacism put them on a crash course with my friends and goals. In my post game, I am actually kind of carrying the fire of the Brotherhood. I use their gear and like to think I am my own personal splinter group of the Brotherhood, in the same vein as Lyon's group. To that end, I wonder if we might see some dlc that will allow us to rebuild the factions we might have destroyed. In the case of the Brotherhood, we get the opportunity to make our own splinter group and set a new standard of goals for the organization. In the case of the Institute, maybe we start to recruit intelligent scientists around the Commonwealth and work toward making synths fully human (or as close as possible) and repurpose tech across the commonwealth to benefit the citizens. Maybe even retool older generation synths to be a militia for the Commonwealth and fight back against the super mutants and ghouls and raiders.
I realize the Minutemen fill this sort of general good group for the Commonwealth, but I really respected the dedication, determination, and purity of purpose that the Brotherhood had. I felt more aligned with their drive to destroy the evil that plagued the people of the Commonwealth, but that ask-no-questions methodology and hardline on non-feral ghouls and good synths drove me away. Right now I am pretending that I have taken up their mantle a little bit and am a lone "white knight" in the wasteland. It would be great to have that realized in the game as an actual option though. It would even pose a great chance to have you make a new choice after you've sided with your group at the end. I told Desdemona that i was done with missions after the last quest, and honestly I kind of was. I had done what I set out to do and we had to kill alot of people to do it. Maybe having the option to rebuild an organization from the ruins of what was could be a chance to let us take what we liked about an organization and make it better fit the ideals it SHOULD have had from the beginning.
It would be a fun and easy dlc I think!