I think the story for Fallout 4 regarding the whole thing with your son being older than you and having grown up to run some shadow-organization is decent and interesting, but when you role-play different kinds of characters, it's not always the kind of story you want.
Sometimes, for some kinds of characters, it doesn't really fit them to have an arc that involves weird emotional drama about your natural son being a 60yo mad scientist, or to have to confront weird metaphysical questions about whether or not a synth-recreation of your kid can be considered your kid.
So here's what I propose, a mod that changes a scene or two, and chops a lot of options out of the main story and resets expectations, rather than your son being taken 60 years ago, he was taken only 10 years ago, as you were at one point lead to believe, he's still a natural-born human being, kept at the Institute, and you've got to save him, like you thought you were going to do.
I'm thinking something along the lines of the story being unchanged up until the "Institutionalized" quest. When you find child Shaun, the room he's in may have to be re-designed. Maybe he would still refuse you believe you're his parent, or maybe it would be possible to convince him you are. Either way, as you're talking, you get interrupted, synths storm the room. Once you dispatch them, the room gets locked down, you're separated from Shaun, and you have to escape.
I guess the whole thing was some kind of trap to catch you for your DNA or something, or to kill you to replace you with a synth, it doesn't matter exactly why. The "Father" character could either exist only as a voice trying to lure you into the trap, or could be cut from the story altogether.
Presumably, there would be no way to join the Institute in a story like this, nor any way to infiltrate it for the Railroad, so you'd have to do the Minutemen or Brotherhood branch of the story from there.
Once you've stormed the Institute, "Father" would presumably just not be there. You get to re-unite with child Shaun, who is never implied to be a synth, he'd be presented to you as still being your natural child. Maybe you'd have to try again to convince him you're his parent, or maybe we'll just assumed he "figured out" that you were telling the truth in the meantime, doesn't matter too much.
That's a rough overview of the idea I have. I think it's a way to re-write the story to be a dumber but more straightforward "rescue your kid form the creepy bad people" story, which may suit certain role-player more, without being completely impractical. I don't think it would require mountains of location-reconstruction, crazy scripts and quests, or massive re-mixed dialog trees, etc, so it's something I hope could be reasonably doable, if someone with the talent was to agree.
Feel free to tell my your thoughts on how a story re-write like this could be improved. Are there any writing or logistical problems I haven't considered? Thanks for reading any maybe considering my ideas.