Late on the subject, sorry. Little things that would have been interesting, other than a script doctor to proof read the story. I may have already submitted them elsewhere on the forum, not really sure. If so, sorry for the repetition. But anyway :
1 - Play as a reporter. Interview important people from various factions, and write articles using the dialog system, basically like you do in the actual game with Piper. Several times. With the possibility of taking sides, which change how NPCs react and comment to the factions, through their idle lines, scripted events, barter prices and quest givers. Depict the BoS as invaders, or praise them as saviors. Deny the existence of Synths, or at the contrary, show proofs of their activities. Use a camera as a weapon. You're in the middle of a war, you could use your gun... but you could also take the risk of using your camera instead. That gives variety. A moral choice. The possibility to play a peaceful character while engaging in violent situations. A new and original way to have a direct effect on the world around you, other than just doing quests. A reason for meeting important people from the factions (interview them). This system replaces the karma system. Instead of your own karma, you now manage the karma of factions.
2 - Make Synths buggy. Don't ask us "do machines have souls?" if it's only to shove a definitive answer down our throats until we choke on it... No, instead, ask the question, and let us decide. Let us doubt. Yes, synths dream, but it's always the same dream, over and over again. Yes, they show empathy, but they also suddenly bug and change their entire personalities. Valentine is helpful, but he often gets "blue screens" by sending you on cases he solved decades ago, by forgetting who you are, by shuffling same answers etc. The Institute's courser "likes" bad actions, then suddenly "hates" them. Curie runs to a guard to say you kidnapped her, all of a sudden, because she suddenly forgot who you are when her OS rebooted. In other words, make us doubt, so that we can think and form our own answer.
3 - Give the Institute a biological Artificial Intelligence, running on biological organs. A biomass acting as a central CPU, capable of dealing with abstract concepts. That would be an interesting achievement, and show that the Institute actually has the potential of doing something.
4 - Replace Ghouls with Institute's test subjects. Humans screaming in pain and sorrow, electronic parts popping from their skin, cables in their organs, rusty bionics at their limbs etc. Excellent salvaging/loot source if you're looking for mechanical/electronic parts, but it would require you to ignore their pleas for help as they charge you. Gives the Institute a whole different aura, brings a new kind of enemy, enhances the thematics and is way more original than zombies.
5 - Like in Silent Hill 2, these new "ghouls" disturb your pipboy's radio, making it actually useful, gameplay wise. When it goes all creepy and scratchy, these guys are around. Makes the dungeons actually scary.
6 - Replace jazz with Irish folk music from the 50-60's. Replace caps with baseball cards.
7 - Travis is a quest giver. You can bring him tapes, which will then be played in the radio. The radio's playlist expands because of your actions, and you can actually personalize it by choosing to bring jazz, classical or folk music to Travis, depending on your taste.
8 - Super Mutants are war refugees from the Capital Wasteland, instead of Institute's test subjects. Many are accepted in settlements, working in farms, as bodyguards etc. Some others want to regroup and go back to war. They recruit. That's right. Super Mutants recruit humans, and they actually run gangs.
9 - Move the Institute away from the CIT. They are under the glowing sea, where they are actually safe. People have dug the CIT, and they found nothing. All the same, move Virgil away from the commonwealth. You have to lure him to make him come back, by broadcasting a signal through radio towers you have to find and fix.
10 - The Commonwealth is empty and has raiders because it's in quarantine. There's a plague going on. A plague that affects mechanical and biological. A mechanical virus, that makes the machines... evolve. The disease is carried by Synths. There's now a reason why robots have personalities, and now there's a clear reason why people are terrified of synths : they are their dead loved ones, walking the earth, spreading a plague. Against their will, of course. Plague was released by the Institute's AI.
Know what that implies with Liberty Prime, right ? He could get SICK. Turn against its creators... Or become something even better. Is that a risk you're willing to take ? Is that heresy, according to the brotherhood's codex? Witness theological discussions about the subject. Settle an actual theological crisis within the Brotherhood, like the one between the orthodox and the catholics about the icons.
11 - The T60 is a BoS invention now. And it's a mix between the Enclave Armor and the Brotherhood's. Why ? Because of the game's cover. It now features this new armor, like in all previous titles, but this one hints that maybe the Brotherhood has become the very thing they fought against.
12 - The railroad doesn't just act for Synths : it smuggles goods through the quarantine lines. They have the best equipped traders of the game, for that reason, but they also put the country at risk, with their constant breakings of the quarantine law. That gives the players the possibility to join them, not by ideals, but by greed for better equipment and easy money. Same goes for the Institute : you could join them, not only because of their ideals, but because they can make a Synth out of your wife's dead body. With all her memories intact. Won't even know she's a synth. But they need your help beforehand.
Gives the player more freedom and roleplay, even when joining factions defined by ideologies.
13 - Gunners are mercenaries working for the Ronto's industrial conglomerate. Their mission is to seize the commonwealth's factories.
14 - Mama Murphy is no longer a member of the Minutemen. She is a travelling prophet, worshipped by raiders. When she is around, raiders are pacified and will not attack unless provoked. You can manipulate her and use her, for actual, direct gameplay. You could use her aura to prepare a surprise assault on a raider's camp, for example. Oh, and 50% of her "prophecies" are simply false. Make us doubt about her powers, instead of throwing magic into our face because "the story demands it".
15 - There are pre-established settlements, now, occupied by raiders. Some missions for the Minutemen consist in assaulting the cities, free the hostage, and be careful with the hostages. Depending on the civilian casualties during the assaults, the citizen could slowly come to love the Minutemen, or hate them! At some point, the gunners even stage a full massacre signed by the Minutemen, to lower their reputation. You, as a reporter, cover the event, and show it under the light you choose. Gunners could pay you to tell their lies... Will you be a corrupted journalist, or a moral one ?
16 - Add a new raider faction to the level list : the vault rangers. They are like the Stalkers from Metro 2033, scavengers roaming the surface, gathering material and goods for their vault. They are extremely aggressive, shoot on sight with modern firearms, and wear Hazmat suits with the typical blue/yellow pattern.
17 - Piper is not a companion. She's a quest giver, an important political figure (as she prints magazines and the local money, aka baseball cards). She runs for mayor. She has a bodyguard, a smart Super Mutant. She is important, influential, smart, and possibly manipulative, depending on the point of view. She doesn't want to "reveal da truth", she wants to impose her truth, by all means necessary.
18 - Show Maxson's bionic augmentations. His brain is connected with cables. Hint that maybe, he too could get corrupted by the Institute's plague. Or maybe, his actions are guided by the calculator ? Make us doubt about the truth of his faith and his orders, only to reveal that no, he has never been corrupted, neither by the Institute's AI nor by the Calculator. He's simply a zealot.
Paradoxally, he's just human. Despite his bionic nature.
That enhances the thematic of the game : when a man's nastiness paradoxally becomes a proof of his soul.
19 - Maxson is not backed by the Californian BoS anymore. He is backed by the Midwest Brotherhood. They agreed with Lyons' views, and have every reason to push Maxson into action against the Institute. They have the calculator. They are afraid that the Institute could reach it at some point, and make it do things. You never see them. You just know that they are here. Fans cry in joy, and Todd can tell us sweet stories about a potential DLC with the Midwest, which would never happen of course.
However, you do witness the end of a communication between Maxson and a holographic screen showing the calculator. The calculator talks down to him. Gives a whole new perspective to his authority, and his free will.
20 - Diamond City has metal detectors at the entrance, and guards randomly "test" you with metal detector devices, giving a layer of paranoia into the game.
21 - Curie is not "a companion". You are her companion. Her quest is objectively 100x more important than yours. She could heal everyone. She's a tribal legend, the "the angel of steel" that heals people with her hands. She may not even exist, until you realize that she's more than a myth. And when you meet her, your mission is to protect her until she reaches the EPA's facility, where she can find all the plants she needs to make new meds.
22 - You don't get to bring Hancock into Diamond City, or your Synths companions under the nose of an high elder. If you try, the guards/paladins stop you and throw you into jail. Can't believe the jail system from TES wasn't implemented into Fallout 4, especially considering that the prison was actually made into the game, and served zero purpose.
23 - Cleaning Cait's blood from chems is only the first step of her recovery. You'll have frequent speech check afterwards to motivate her and convince her not to take chems again. Because cleaning the blood from chems don't do shit for addiction, it's just the first step. And because it would give speech more value, while adding more "life" and interactivity to your relationship with her.
As for dogmeat, you have to actually train the dumb mut so that he can track smells, bring objects and do tricks. At the beginning, he's almost feral and he actually bites you several times. Your choice, either to beat him or to be a good master and help the dog recover from his trauma (he's no longer Mama Murphy's dog, in this version.). You need to find trainers to help you train him, which leads to interesting, yet light moments of interaction.
These ideas keep the current storyline almost untouched, and don't require to change the setting or to do radical changes in the script, except for the radio thing.
