Now that I read the last few weeks I think I agree with everyone. The way the story culminated seems forced and unnatural. I think it could have been a lot better with the following changes:
1. The railroad was a respectable attempt at creating a synth-friendly faction, but I thought it felt flat. The idea of humans forming a secret society to help Gen-3 synths by wiping their memories and secretly integrating them just made no sense and was very uninteresting.
It would have been more compelling if it was instead a Magneto-style faction made up of Gen-3 Synths who were trying to build up a free-faction of synths. As part of this quest line you are mind-melded with a synth (Nick Valentine style) and the quests center around fortifying your synth base + stealing synths back. The synths inside would be disagree with eachother on what to do, with some synths wanting to segregate from humans, others wanting to integrate with humans and others wanting to control humans. You can then choose which path they follow as part of the end-game.
2. Like most else I thought the institute was confusing. You spend the first half of the game seeing the synths as sort of boogie-men, with gen1/2s being pathetic fighters, and gen3's being sleeper-cell terrorists and the coursers being these elite commando ghost guys. The institute are clearly acting like bad guys, what with ruining your settlement's happiness for no reason.
Then you find the Institute and they're all about isolation except when they absolutely need resources above ground. So why do they send their synths out to cause havoc in goofy ways? Who knows. You get very little idea of what the Institute wants to do, and you as director never get to really direct anything at the end. You get to play a message to the commonwealth, but it's ambiguous and disconnected from what folks internal to the institute feel. It would have been nice to be able to choose to integrate with the topside after becoming director.
3. The BoS had a very compelling argument that was underpresented compared to the raw bigotry they had. The synths, or strong AI in general, present an apocalyptic risk to mankind for all the reasons we've been theorizing about for a century now. The BoS instead focuses on how synths, and ghouls, and super mutants,and jews,and blacksare abominations and should be exterminated. Maxson's handling of Paladin Danse was a good example of this. Maxson's clumsy attempts at getting the player to kill Danse, and then his derision of him afterward makes little sense unless Maxson is a foolish bigot, which I don't think the character is billed to be. If instead Maxson showed compassion and sold the idea of Danse being a possible tool of Synths/Institute, it would have made more sense.
Either way I thought the BoS played its part fine but could have been more enjoyable as an intelligent and tough force instead of just the fourth reich.
4. The minutemen and the settlement system I thought were a good effort. I didn't think the minutemen belonged with the other three factions and should be considered separate and not mutually exclusive. It was that way with the institute ending. I wouldn't really have changed much with them. Though I think an excellent opportunity for a community mod effort would be to flesh out the settlement/minutemen system to be able to essentially repurpose many locations on the map + terraform the settlements. Instead of just setting up shacks in the wilderness, being able to reclaim a water treatment plant, a power plant, steel manufacturing plant, electronics factory etc etc and create a new civilization would be interesting.