In Fallout 4, I really struggle with siding against the Brotherhood. Not because it's the Brotherhood, I hate what they stand for, but because it means I have to kill Scribe Haylen. She's a good person and a sweet girl who really cares about her comrades. If you join them before deciding to fight them, it feels like you have to kill a friend. More than that, it makes you realize that a LOT of the regular soldiers you're killing are probably good people, as well.
In Skyrim, when that one group wanted me to kill the Dragon that had helped us. Jeez, I did not want to do that. Like, at all. But, I did it, because it seemed like the smartest way forward. I felt so crappy afterwards, though, and looking down at the Dragon's dead body, I though, "my character would not do this." So, I reloaded, and kept him alive. Next time I played, I used a mod that let me have my cake and dragon, too.
IIRC, Fallout 4 had a cut option where you could get Danse to revolt against Maxson and ptentially become the leader of the brotherhood. This really would've redeemed the brotherhood for me. There wasnt really a right choice IMO. The Brotherhood would be the equivilent of the far right, while Railroad are basically social justice warriors. Minutemen felt the most correct (their focus is on protecting the people), however their questline is boring AF.
As for Skyrim, it's funny, I killed the dragon too, and then reloaded my save afterwards as well. Screw the Blades.
Bet with Intrinsic:
The Switch will outsell 3DS (based on VGchartz numbers), according to me, while Intrinsic thinks the opposite will hold true. One month avatar control for the loser's avatar.