That's not enough to fix your bad writing, lack of real care about this franchise, and all those lore inconsistencies you made, Mr. Pagliarulo.
Well, I might as well do it since I don't see a reason not to.
The C.T. Phipps Rewrite of Fallout 4
+ The Sole Survivor is returning home to visit their sibling after being the only one of their unit to survive an ambush by Chinese communists. You can also talk with your sibling about the horrors of the war in Canada as well as what you think of the government. She then reveals she's signed you both up at the local Vault. You also get to meet with her son, your nephew, Shaun, who is the age of Synth Shaun.
Gameplay Change: Same system from Fallout: New Vegas only with the VATS change to bullet time versus turn-based combat. Karma is still absent.
+ There's a bit more inside the Pre-Great War Period and you can go across the street to talk to your neighbors and get a bit more information about the world. This is all optional but you can even do a few quests around the neighborhood of Sanctuary Hills for minor EXP.
+ If you dawdle running to the Vault, you see the Boston Nuclear Bomb go off and die.
+ You get frozen in your Vault and then awaken to find everyone missing. If you get the Overseers recording, you find that everyone was evacuated from the Vault except you. Your sister objects and is killed in front of your frozen pod.
+ You escape from your Vault and proceed to find Codsworth who directs you as normal to Preston Garvey, only Garvey is under assault by
Maccready's Nuka Raiders. You can either side with the Minutemen or the Raiders in this with some hints this is more complicated than good or evil.
+ The Nuka Raiders quest will take you to a base on the East side of the map which will have Colter as the Boss. You have the option of then doing the Evil version of the Minutemen takeover as you eventually retake their fortress and unite the Commonwealth under the Raiders. You can also eventually challenge
Colter to a contest to take over the Nuka Raiders in the Capital Wasteland. To actually visit Nuka World, though, you need the DLC.
Lore Change: The Gunners are simply absent from the game as they are very very bland.
+ With Shaun now "just" your nephew and not in any immediate danger, you can follow up rumors of seeing the visually distinct Kellog walking around with a boy about Shaun's age and description. At one point, you'll be attacked by a character identical to your Sole Survivor and if you destroy him, he becomes a bunch of circuitry and parts.
+
Lore Change: Synths are androids in this universe rather than clones or artificial humans as while it's easier to detect them, it makes the technology a bit easier to stomach and the question of sentience more pertinent.
+
Gameplay Change: There are only a few settlements you can build in the game with Sanctuary Hills and Starlight Drive in being the only ones which are related to the Minutemen and Raider stories. The Citadel is one you can have repaired but you purchase the repairs there. Later, you can unlock Spectacle Island as a bonus for those who love building. Home Plate and other houses the PC can unlock can be decorated ala Fallout 3.
+
Exploration Change: There's less "empty farms" this time around and a lot more interesting stuff going around. For every settlement which no longer is built, there's a small town or village with a side-quest related to it.
Some minor thoughts:
* Goodneighbor is much larger and freaky weird.
* The Slog is being harassed by the Brotherhood of Steel and bigots
* The robot greenhouse actually has some defenders.
* The farms have quests about Raiders, Super Mutants, and so on.
* Lots more awareness of groups and their dangers.
+ Eventually, you reach
Diamond City and the plot continues onward to
Kellog where you have the option of either avenging your dead sister or sparing him. If you spare Kellog then he becomes a Companion and fills you in on the Institute vs. diving into his brain.
+
Lore Change:
Shaun was adopted by the Institute's director after murdering your sibling. He was raised with the Institute's beliefs which reject the Previous Pre-War world and believe in creating a world ruled by SCIENCE and utopianism. That's why you, the veteran, were left behind. They don't use direct violence but infiltrators, kidnapping, brainwashing, and so on to control the Commonwealth from below.
Shaun is actually a fairly new Director and the former robotics head. He's not dying and his first act upon awakening is to release you and try to get you to avenge your mother. Synth-Shaun is actually just a way to give clues to have you hunt down and murder Kellog. He's disappointed if you don't.
We get some hints the Institute is actually responsible for some good in the Commonwealth like the fact they created Diamond City, actually tried to help the Ghouls, and have been steadily helping rebuild the Commonwealth. The Super Mutants of the setting are refugees from the Capital Wasteland in this setting, not made by the Institute.
+ The Glowing Sea *WILL* kill you if you're not in Power Armor (which renders you immune). It's also leveled for levels above you.
+
Virgil was experimenting on how to CURE Super Mutants not creating them.
+ The Brotherhood of Steel arrives in force because of the discovery of the Institute but an investigation of their terminals and arguments are they're here because they see the Institute is a threat to their power and they intend to annex the Commonwealth. Maxson doesn't think of Danse as a genuine person as a Synth but can be convinced to release him back to the Brotherhood or Danse to challenge Maxson for leadership of the BoS.
Which is resolved...VIA SPEECH CONTEST AND DEMOCRATIC VOTE!
+ Notably, in this version, Arthur Maxson is a more nuanced character and something of a paper tiger while Danse is a superior leader but not someone who really wants the job of the main seat. For progressivenesses sake, I also think it'd be fun to make them lovers and their relationship broken off ala Veronica and Cynthia.
+ Lots more references to Fallout 3 and the Capital Wasteland in this version.
+
Gameplay Alteration: A lot more quests are resolved via High Intelligence, Perks, or otherwise.
+ Radiant quests require you to speak to someone other than your Companion.
+ The Railroad isn't a faction which can "win" as in this game, eventually either the BoS or Institute (whichever you don't side with) exterminates them.
For PATHOS!
+ You can get married ala Skyrim at the Diamond City chapel with special dialogue for marrying multiple partners, the proposal, and other bits of fun.
+ Combat Zone, Racetrack, and other locations are all up and running in this version.
+ The Cabots are just a bunch of 2050 chemists and inventors rather than ALIENS.
+ The final battle is between the Brotherhood of Steel and Institute with the option of Raiders or Minutemen destroying both. You can also choose to lead a Synth revolt during the events as afourth option.
+ If the BOS win, they take over the Institute and patrol it. If the Institute wins, they proceed to take over the airport and start experimenting with Liberty Prime.
+ Synth Shaun is just an unimportant machine but can repair items to 100% and other useful things if you set him up at a settlement. He's a boy who will never grow up or out of his childhood programming, though. I'm almost tempted to make him a companion, though, just because a 12 year old robot murdering people says "F-U" to censorship.
+ Ending Slides based on what you did before the Final Battle.
