I completed the main quest at around 35 hours. It has potential, but I felt like it fell a little flat. Part of the problem may be the faction I chose to back, but I wonder if any of the others could possibly be any better.
Here's the story in a nutshell:
You're an average Pre-War schmo, with a spouse and a baby. You've been selected to go into a nearby vault in the event of a nuclear war. The nuclear war happens, and when you get to the vault, you find that it's a shady cryogenics experiment. You're frozen for some indefinite period of time. At some point, you wake up and see that your spouse and child have been unfrozen, and a lady in a creepy white environment suit and a grizzled-looking mercenary dude take the child by force, killing your spouse in the process.
The cryogenic pods are started up again, and then some time later, you wake up again, but this time the door to the pod opens. The vault is completely abandoned, all of its inhabitants dead. Of the various people in the cryogenic tubes, only you survived.
When you emerge from the pod, you see that the world is a blasted wasteland, one in which you have to strike out and find your kidnapped son. During your epic manhunt, you discover that your son was kidnapped by the Institute, which is like a boogeyman to the people of the wastes, due to their habit of making lifelike robots that infiltrate human society, and that your son is not the first person they kidnapped.
It also becomes apparent that years have passed since the kidnapping, and that your son is at least 10 years old. Long story short, you join up with one of the Institute's many enemies to raid their base and rescue your son . . . only to find out that 60 years have passed. Your son is now a grey-haired adult man, and, in fact, the head of the Institute, who had hitherto been your sworn enemy.
That's where the story falls apart for me. The problem is that you've been led to believe that you're playing out a revenge story, but then things get way too complex for that. This, of course, could be the foundation for a much better revenge story, but it doesn't quite prove to be complex enough for that. The writing feels really strained, and there's never really a satisfying emotional payoff.
The way I see it, the Institute doesn't stop being your enemy just because your son happens to be in charge. Yet your son doesn't stop being your son, just because he's 60+ years old and the leader of the villains. A good story about this situation would be about your attempts to thread the needle, establishing a relationship with your lost son while attempting to preserve your principles.
And to be fair to the game, it at least seems to try. Your son is pleased to see you, and immediately invites you to work for the Institute, explaining that it has a noble purpose, and that he feels more like he was rescued rather than kidnapped. This could be interesting, where you start off a little dubious, but willing to compromise your principles just a little for the sake of family, but then gradually have to face the fact that your son's work is unconscionable.
Unfortunately, this character arc spans exactly two missions. The first mission your son assigns you is to track down and capture a rouge synth (android) who has become the leader of a band of raiders. It's already been established that the Institute uses synths as slaves, and that many of their more advanced models are fully sapient, so it's a little tricky ethically - you're returning a person to slavery, but he is a bad person who deserves it.
Your second mission is to assault an abolitionist stronghold and recover a group of escaped synths who, when you finally find them, are terrified of going back to the Institute and beg you to let them go. And at this point, I can't help but think about Kellogg, the mercenary who kidnapped your son and shot your spouse. Thus far, he's loomed large in the story, even after his death, a figure of legendary ruthlessness and cruelty, and my thought was "oh shit, my son is trying to groom me to become the next Kellogg."
That's a neat idea, but it needs room to breathe. The confrontation between parent and child comes too fast, and the falling out between them was almost immediate. It would have been nice for there to have been time for a bond to grow between your character and their son, one that was undercut by his creepiness as the head of the villainous organization. Maybe I just picked the wrong dialogue options, but there didn't seem to be any of the ambivalence I would expect from someone thrust into this situation.
But I could probably have accepted that as video game shorthand, if not for what happens next. After he abandons you to go back to the Institute, your son orders a military attack on the faction that helped you find him in the first place. In my case, it was the Minutemen, a group of do-gooders committed to fighting the raiders and making the wasteland safe enough to reestablish civilization. It was a completely unprovoked assault that was beyond the pale, ethically.
So, of course, there is a counterattack, and because you're the player, it's extremely effective. You manage to destroy the Institute's primary (and only) base, and as you're on your way out, you find your son, confined to a sickbed and possibly dying . . . and the confrontation between the two of you completely misses the point. You don't even get a chance to offer to rescue him from the upcoming explosion, only to be rebuffed (or, at least, I didn't see one, and I was looking for it). It's just such a basic oversight.
The last conversation doesn't even address the subject of anger. Not from a character perspective - your son knew who you were working with, and basically tried to have you killed, nor a player perspective - the assault on your allies was a really tough fight, one that consumed a huge amount of precious resources and left my power armor wrecked, nor from the intersection between them - you've just spent all this time with your son as a MacGuffin, and when you finally find him, he's an unctuous twerp. I'd have really liked to have some closure on that issue.
Finally, the biggest sin of the ending is that it doesn't give you an epilogue. Do the Minutemen succeed in rebuilding the Commonwealth, what happens to the Institute survivors you went out of your way to save, does the Brotherhood of Steel continue to cause trouble? We may never know (though, I suspect there might be a different ending, depending on what faction you choose).
Overall, I wouldn't say I hate the game's main story - you get to meet some cool characters along the way, and there's some fantastic spectacle - but it definitely falls flat when it comes to emotional nuance. Luckily, the story is not really the game's main draw. Exploring ruins, killing monsters, and hoarding junk are more fun than they've ever been, and that's easily enough to sustain me for 30 hours more.
(yes, it really does look like it's shaping up to be that long)