This is my second run, this time as a Minuteman General who kept only the Minutemen and Railroad alive. The two other factions were wiped out from the face of the Commonwealth, and there were a lot of difficult decisions to make.
All of the decisions were my character's, not mine.
Backstory: I did a massive headcanon just to bring my Lone Courier into the Commonwealth. She went there because she remembered what Dr Zimmer told her about the Commonwealth, not knowing she was going to be entangled into yet another faction conflict.
Several months after the Battle for Hoover Dam, Princess Cathy was craving new adventures. She appointed her friend Brisa as her successor, knowing that she may be gone for a while. Luckily, she had good dealings with the Enclave Remnants and asked them to fly her over to the entrance of Vault 111.
Close by, she saw the body of the Sole Survivor. Being curious, she took everything from the body, including a strange holotape. And of course, Cathy put the holotape in her PipBoy and started to live the SS's memories up until the point where she exited the vault.
Codsworth, for some reason, thought that Cathy was the SS. Cathy got fed up of trying to reason with him, so she played along. She actively lied to everyone, saying that she wanted to find her son, but in reality, she just wanted to find the Institute that Dr Zimmer described to her. And so she got entangled with the faction conflict.
Railroad: Cathy thought that their cause was noble and just, and didn't find anything wrong with their philosophies. So she made friends with them and ordered the evacuation signal when she destroyed the Institute.
BoS: Cathy has a rose-tinted view on the Brotherhood, thanks to Lyons. She destroyed the Mojave chapter because they were a threat to her future plans, much like Mr House thought as well. She was disgusted that they believe that all ghouls and synths should be wiped out.
Even after Blind Betrayal, she decided to give them one last chance. Until she was given the order to destroy the Railroad. Cathy didn't want anyone harming her friends and it didn't help that they were also hostile towards non-humans, so she destroyed them.
Institute: At first, things were going fine. Cathy really thought that becoming leader would mean less violence.
Nope.
Father had the audacity to give her an ultimatum - destroy the Railroad or don't come back.
So she shot him in the face, but beforehand she told him that his mother was dead a long time ago and thanked him for being an idiot for falsely believing that she was his mother.
When she left, a scientist shouted at Cathy for "killing her own son". It was the time when she exclaimed that she was never Shaun's mother in the first place before relaying out.
Minutemen: Even though Preston can be really annoying with tasking her to clear the same place twice, their views on a better Commonwealth coincided with her's and that was building strong settlements and protecting them when things get rough.
She reasoned that Institute kidnappings may spread to her settlements and that the BoS would target the ghouls and synths who seek safe refuge in her settlements.
Mystery behind the "I'm not your mother" was solved: Apparently, the holotape had an invisible field which manipulates people into believing Cathy was the SS. Cathy didn't know why the SS would do such a thing as that just remains a mystery. A mystery solved, another one opens.
Musings: Difficult choices all-round. I would've loved to keep everyone happy but that's not realistic, so NV-style, I had my legacy character pick the Indy option a second time.
So far the playthrough is just under 1.5 days and there's still a lot to see and do in the Commonwealth. I can see Cathy marrying Piper in the future, either through a DLC or mod, but for now, she's tired of fighting and she was glad that the SS's holotape was destroyed when the Institute was destroyed.
I still think Father and Maxson are the most unlikable characters in the game and I had no remorse when both were killed by my character's hand. And that there was some potential with the factions which were, alas, not realised in the final version of the game.
I actually think that despite the forced backstory which I had to headcanon away, the voice which I modded away and the dialogue wheel which I modded away, Fallout 4 is a great game and can only be made greater with mods and DLC.