There's no real point in overhauling the story. Fallout 3 adds nothing of note to the series, instead rehashing the same old stuff, but worse.
It would be far easier just to write your own story, then make good writing out of the mundane mess Bethesda made.
EDIT: ThatZenoGuy is a ninja
You are correct, but this is sad actually.
Look at Moira Brown quest, Wasteland Survival Guide. It interconnects most of the game world, it connect quests, it starts different quests, incentivize the player to explore and engage in different things. And if you chose to concentrate only in the quest rather than the rest, it rewards usefull things for your character.
Also her character is pretty interesting and questioning about her motives give you answers why she's writing the book. I'm not talking about the quality of the writing, wich it could have been better, but the quest and character ARE structured and have meaning.
So yes, Bethesda know how to make a RPG quest that isn't entirely dumb or meaningless.
Now, look what they did with the BoS. Yes, the BoS portrayed in the game is bad, really bad.
The idea however, is not.
You have a group of fanatics bordering the nazis (because that's what the BoS is), where their leader had a change of heart during the course of a mission. Instead of collecting technology he decided to entrench in a location and try to change the forces and politics dueling in the area.
This also leads to a split in the group, with some members going their separate ways and calling him a traitor that belongs in front of a firing squad, while some of his remaining soldiers question themselves if they did the right decision.
He also breaks most of the sacred creeds of the BoS, like not allowing outsiders to enter their ranks for the simple reason of bolstering their numbers and not being involved in outside concerns beyond their own.
And that's it. The rest of the game wastes EVERYTHING of interesting this setting could have been.
You could have even linked the Pitt to the main game, maybe that's the reason why Lyons stopped in DC and changed the BoS direction. At the same time you could've explained why on earth they performed the Scourge in the first place and what they were looking.
But no, let's make them a childish group, with childish reasons for doing what they are doing and slap a broken morality to it... for reasons.
FO3 has this nasty habit of good/bad karma that ruins the quests most of the time, it's one of the reasons things don't work, because Bethesda decided to substitute meaning, motives and dialogs by it.
For what end I do not know, because there are a lot of fuck up things in the game distorted as good or bad.
