1. Make FO3 to your liking
2.
3. Profit
Oh, let me tell YOU what I would do! Since I'm in charge of anything I want, including writing, I would need only pay for another writer to assist me by pointing out flaws and plot holes in my story.
This implies that mankind is better adapted to reconvene their selfish savagery rather than wear the failed mask of civility. Don't try to convince others that you are noble when it is so clear to the senses that you are a selfish bigot with a sense of entitlement. There are no benevolent protectors or decent wastelanders. The theme is not survival, but selfishness. You are selfish. Your neighbors are out for themselves. Your pastor does not do his job because he wants to help others, but because it satisfies his need to feel powerful. A wasteland dog does not hunt molerats because it is hungry, but because it knows that it is making what's left of the world into a worse place. The children are future criminals, and there are no Agathas but only different extremes of Nathans.
In this post-apocalypse nothing is done without tribute to someone's ego. Merchants will not sell to someone unless they entertain them by groveling, kissing up, or tolerating verbal abuse. The pastor requires "donations" and praise for his interpretations and interpolations. The locals pay tribute to the mayor or elder by having their daughters kiss his feet, annoint them with their tears, and dry them with their hair, or some other symbolic act. The mayor or elder has jurisdiction over their domain, not because they are lawful like that sheriff in Megaton but because they have the support of manpower.
Every town / tribe lives by the rules of the leader, and in none of these places is the First Amendment acceptable because it inspires treason and heresy. The Equal Protection clause is unconstitutional. If you have a problem with a man you duel them, and if that man is the elder then you duel his champion. Otherwise, go somewhere else fast. A settler need only concern themself by meeting settlement's supply and by reporting lawbreakers and heretics. The merchants distribute food in return for competitive good word and protection from slavers, as well as report rumors to the mayor and pick his women for him. The mayor and his men protect the settlement and send men to the higher factions so that there are more unattached women. The pastors appeal to the mayor for his mercy or his judgement in a dispute.
And of course all tribes / settlements are in competition with each other for permission from a higher faction to expand their borders. So from the tribe leader down to the begging settler it is a showdown over whose town is the greatest, which one has the best rules to live by, which is the richest, which is the smartest, which has the least heathens, etc. The faction leaders don't care as long as they recieve bi-monthly tribute in caps and men to fuel the war with supermutants and other factions. I forgot to mention that the mayor's men usually have ghouls manning the jobs of executioner, interrogation, intimidation, etc.
tldr:
Well why did you read it, then?
So what would Fallout 3 have been if you were the lead designer?
Important Edit:
There is no cowboy music. Instead it is war drums.