(Massive spoilers ahead. Obviously.)
As is typical with most RPGs, Fallout 4 has a healthy array of factions to choose from on your quest to save Shaun. And like almost all RPGs, the main quest itself isn’t exceptionally detailed or story intensive for the sake of having the story spread out among the other things you can do in the game. After all, one of the main draws to such games is that you choose what kind of a story you want to hear. Unfortunately, this does leave some holes in Fallout 4’s story, regardless of how you want to play it.
Wait, who are you again?
Fallout 4 starts off with your baby son being kidnapped and your spouse murdered by mysterious figures, which naturally leads you to go explore the remains of the Commonwealth to look for whoever committed these acts. This results in you meeting every major faction in Fallout 4, which is where the story proves to be a bit shaky.
Simply put, none of the factions have any particular moment where they respect your position as the player. All the factions basically make you their errand boy, even if you’re the General of the Minutemen or Director of the Institute. At the end of the day, you are merely following along in a certain story. You will always have to choose at least one faction to destroy, you will never be able to explore major alternatives to what you are tasked with, you never even get a chance to have any particularly emotional moment with your son.
Compared to Fallout: New Vegas, this is a bit of a step backwards in terms of narrative freedom. After all, you could broker a treaty between the Brotherhood and the NCR, bring almost every minor faction into the penultimate battle at Hoover Dam; whatever you wanted to do was reflected in the ending. Even in Fallout 3, your decision to blow up or save Megaton affects your interactions with other characters. Fallout 4 gives you the illusion that you can have a massive impact on the major faction that you choose to back, but you never see it come to fruition.
You’re telling me, but you’re not showing me
In the same vein, you never really get to see the bad side of the factions. Sure, you get to see what happens when a prominent member of the Brotherhood is revealed to be a synth, but what of their biases against ghouls? What would happen if a synth just happened to be hiding in a neighborhood that predominately features normal ghouls or even simple civilians? Would the Brotherhood just barge in, going house to house? Or perhaps even level the settlement to the ground? And what of the Institute and their FEV experiments or their tendency to replace people with synths? To what lengths would the Railroad go to free synths? Is one free synth worth the life of one innocent person who couldn’t care less about synths because they are merely trying to survive?
You never get to question why they do such things, much less see why they do such things, they just say they do it and that’s that. You never get to explore the morals of any of the factions if you don’t want to, and even if you wanted to, you can’t. That is because by the end of the game, no matter what, you are playing as a glorified pawn right down to having to find your son.