To come back to the "how to fix F4", here are some random elements and ideas :
-Do synths have a soul and feelings ? The game gives zero evidence that they do not, and plenty of evidence that they have a soul indeed. This is a slap to the previous titles' subtelty, and it could have been fixed easily : make us doubt. How ? Make Valentine buggy. Make him send you on cases he solved decades ago. Make him forget who you are at random moments, even turning him hostile for a second because he thinks you're a criminal. Make Curie suddenly forget who you are after you banged her, and run to a guard calling you a kidnapper. Make the Institute Courier "dislike" crimes at some points, then suddenly "liking them" and suddenly talking with the voice of a female child. Make us DOUBT to make us think, to make us care. This is how you write a moral question : people need to think, not have the definitive answer thrown at their faces.
On the same subject, make Mama Murphy ramble nonsense at random moments. Never give "proofs" of her psychic abilities, only hints, tainted by doubts. Maybe she has powers. Maybe not. Make that depend on the player's opinions, and in order to have opinions, we must have the freedom to doubt.
-Drop the "this is your destiny" thing. Seriously, stop that. The very concept of destiny is a slap to the face of freedom, which is the main reason why you play an open world RPG. You don't have a destiny : you shape your own. The concept of destiny, in Fallout 4's case, only highlights the linear narrative that plagues the story all along.
If Mama Murphy was wrong about your destiny, that'd be another story. But in this case, she is ALWAYS right, and it just strenghten the feeling of following the yellow, radioactive brick road.
-Make the brotherhood great again, and go all the trump way ^^ more seriously, don't make them blow the Institute. Simply put the Prydwen NPCs there after the ending, and voila.
-The Minutemen : how to fix them ? First of all, let us join the EXACT same faction, with the exact same radiant quests, only dressed up as raiders or gunners and make the Minutemen attack your raider settlements. I'm serious. It's a cheap move, but it gives, at least, the illusion of choice.
Secondly : don't become the General right away. Make the Minutemen obey a shadow figure who calls himself "the general" and only gives instructions via radio. Make us wonder who he is. Make us confront him at some point, and make us able to keep obeying him or overthrow him, depending on your morals. Bethesda can give us the cheap "He was a SYNTH !" twist if they want, it's still better than becoming general after I saved a redneck and insulted his ideals at every occasion.
-Piper : don't make her leave Diamond City. Don't make her a companion, because here, she abandons her family and her business to a VERY hostile mayor, who just tried to condemn Piper to a certain death and threatened to scrap the printing machine for parts. Make Piper give radiant missions of journalism : cover events, give your point of view, affect how the world sees the Brotherhood and the Institute. That would have been simple to implement, that would have made the hero important in a mature, logical way. He has the power to manipulate the masses in the favor of a faction. I would have loved this feature, and it would have enhanced the current "drama" and thematics.
-Make the Brotherhood turn hostile if you bring a Super Mutant, an actual Institute Assassin, two synths or a junkie rebel in front of your military commander. Same for Diamond City if you bring Hancock there.
-Super Mutants ? Make them refugees from DC, and for god's sake, don't make them hostile and racist for no reason. A virus doesn't suddenly turn people racist, a brainwashing does, and Institute's mutants weren't brainwashed, so they have no reason to hate humans at all. Make some of them actually socially accepted, acting as bodyguards for caravans. It would give a more "morally grey" aspect for the BoS, since they kill them on sight, hurting the caravan's business.
-Replace caps with baseball tickets, printed by Piper. This way, Diamond City can make business with traders from afar and the conflict between Piper and the Mayor suddenly becomes a clash of political power : banks vs government. Suddenly, Piper is an important person.
-To hell with the jet, invent a new drug. Here's a new one : "virgin fart", an industrial gas sprayed in the mouth with a spraypaint, discovered by the workers in Ronto or Pittsburgh, working in the fumes of the industry. I litteraly just made that up in 10 seconds. Hire a professionnal writer, a script doctor and make them sit in a writing room for an hour : you'll have 50 other substitutes for the Jet, way way better than the one I just made up.
-Put the Institute away from the Institute of Technology, because really, the whole world would have guessed their location in less than a hour. Put them buried under the glowing sea, and move Virgil to the submarine. Here, nobody can reach them. Nobody can think about reaching them. Here, they are safe.
-Take the time to write a final boss. Prepare the encounter. Let the tension rise. Remember your feeling the first time you realized that you had to face Horrigan ? After witnessing everything he has done ? Remember how Lanius was introduced by everyone before you met him ? That's how you do it, baby
-Give actions consequences. I insulted Piper's lifework in front of her enemy ? Oh well, guess she won't help you finding Valentine, then. I insulted Danse's ideals and let him do all the work while I was smoking jet ? Don't make him vouch for a job as a knight in the brotherhood. In other words : you fuck up, there's consequences. That's litteraly the difference between a shooter and an rpg.
-Play SOMA and learn how they wrote a deep, intense moral dilemma about souls in machines. Maybe even hire their writers, they rock and they need money. Also, Legacy of Kain's writers are currently unemployed and looking for a job : give them one. And hire a script doctor to look after the final script, because even the better make mistakes. Even Pratchett hired a script doctor, and she is Pratchett.
-I don't give a damn about synthetic gorillas. If you want to make trendy stuff, make the Institute able to make dinosaurs. That's a demonstration of true genetic power. That's trendy. That would make your target audience root for them, many gamers seem to love dinosaurs. It would be a bit cheesy, but it would also be an awe moment, in which you realize that yes, the Institute can change the world.
-Drop the Synth uprising thing, it's never going to happen, because it can't happen if the Institute is logical : they'd have a general safe button. Make us disable it before bringing the uprising to the table, in the current state, it is broken.
-Make Codsworth unable to "like" or "unlike" my moral actions, because he's not an IA, he's a domestic cheap robot. It's one thing to have a personable toaster, it's another thing when my toaster starts lecturing me about morality.
-Replace Ghouls with Institute's escaped test subjects. Make them zombies with mechanical and bionic parts hanging from their deformed bodies. Don't even change their animations or scripts or anything, just the name and the texture for pete's sake. If a modder can do it, a studio can do it.
-What purpose does the pre-war introduction serves ? If you really want a pre war sequence, make it through virtual reality, which would be used by vaults to educate their children about history. Make us born in a vault. Remember that in Fallout 1, we learn that robots take care of the birthing. That would introduce us to the game's thematic right away, and give us a subtle, yet efficient contrast with Fallout 3 : you're not in the hand of a loving father : you're in the hands of a soulless machine who pierces your skin with syringues to see if your blood doesn't carry dangerous diseases for the vault. The soulless machine tells you that you are 78% susceptible of dying of heart attack at 54 years old, and 85% susceptible to develop violent behaviour. That's it. A soulless machine told you your intimate future, and then, when you confront the idea of self awareness and destiny from actual synths, there's an echo with your birth. It makes the thematic more powerful, more organic. Oh, and if you pick 1 in intelligence, the robot drops you and tells that you're now experiencing brain damage.
-Don't make the railroad go after a courser ! Doesn't the courser have a soul, too, in their opinion ? Cannot a courser feel guilt and doubt, if we follow their logic ? Convincing them to rise against their masters should be one the railroad's top priorities. Make Desdemona beg you to try a peaceful approach. Make us doubt about our regular methods and make us understand that no, a mass murderer is NOT a socially accepted person. Anywhere.
-Who cares about the gunners ? Replace them with "Vault Rangers". Yeah, vault rangers. A recon team, highly armed, performing scavenging and scouting tasks for a local vault. That would have been a very original raider faction, and people would have hesitated before shooting at people wearing vault suits, right ? That would have been a surprise, and when I play a Fallout game, I love to be surprised.
-After you find out what the Institute really does, you basically have to roleplay a bad guy to actually join them. Which, in my mind, is a problem. Since you cannot "truly" join them by conviction, give another motivation : the Institute can make a Synth from the deceased wife/husband. Give you your former life again. There, you have a reason to join them as a "good guy". You will have to close your eyes on their infamy and fight your old friends, because your former life is worth more than their pity wars... But what is your former life worth, really ? Isn't it time to let go of the past ? (Yes. Connection to the thematic of the previous titles, like in a proper storyline) Your moral compass will be tested. The drama is there. And in the end, your immersion will be on steroids : a hero fighting for a side while knowing it's the wrong one, is a classic, yet powerful narrative tool.
-Kellogg. Make an option for not killing him. Give peaceful alternatives to the most obvious elements : how on earth am I supposed to progress if I play a peaceful lawyer ? In the current situation, I cannot save Preston. I cannot save Valentine from the vault gangsters. I cannot build the teleporter. I cannot help the brotherhood, the railroad, the Institute. Long story short, it's impossible to progress without turning into a mass murderer, and this is a problem. Could have been solved : I could have convinced Preston to give up Mama Murphy to the raiders. I could have infiltrated the vault gang or lied my way to the boss by saying that I have a proposition for him. I could have convinced Kellogg to turn against his employers and atone for his sins, by my side. I could have convinced the courser to do the same. Nothing "impossible" in terms of production, time or budget. Nothing in the current engine would need to be changed.
-When the guy wants to kill his brother in Diamond City, I cannot do anything. I can kill the guy or wait for him to be killed. Make it possible to intervene : I could convince him to lower his gun and talk to his brother. I could encourage him to kill the Synth brother. Nothing fancy, just a little freedom in the situations would have been nice.
-Please, enough with the mercenaries getting paid to follow you forever without any prior knowledge of who you are and what the mission is. Not a single mercenary in the world would do that. If you want to hire Maccready, get ready to rock at speech skills and pay him every week, or he'll dislike you and leave.
-Cait... Sigh. Great potential. An Irish female junkie gladiator. Sounds fun and quite unique. But, listen, Irish people don't just talk about fighting and getting drunk. They are normal human beings. Also, cleaning the system from chems doesn't magically cure addiction. That's not how it works at all. If it did, any junkie willing to spend three days at the sauna would be safe and sound, because "cleaning the system" is the "easy", first step. That doesn't fix addiction at all, in fact, it makes it even harder to bear, as you are now aware of your brain seeking its daily fix of dopamine. Curing addiction takes a lot of time and dedication AFTER the body cleaning. You know how it could have been translated in the game ? Bring Cait to her magic chair. Yeah, murder 50 people on the way, because your friend's health is more important than them, I guess. And then, random speech checks to keep her from taking drugs and boost her motivation. The speech checks are harder and harder, until Cait is finally cured.
-Make Curie extremely important, not just a love interest. We are talking about the first robot turned synth, and litteraly the one who has invented the universal cure. She is a world savior. She'd be the hero in every story. The one you help, not the other way around. Instead, we are given the infamous humping robot treatment, and it's a great waste of potential.
-If you can't resist the temptation of implementing radiant quests, at least make them fun and rewarding. Here's an idea : the radio Travis quest was horribly written and forgettable. Instead, make Travis give radiant quests : he wants music tapes. For each tape you bring him, there's a new song playing in the radio. You can litteraly make your own playlist with radiant quests.