So, over the course of the main storyline, the player can ally themselves with three different factions. Minutemen, Brotherhood of steel, and the institute. These have different end goals and ways they went on about it, but ultimately all three thought they were doing the 'right thing' for mankind. Institute was the oppressive 'evil' faction, minutemen were the stereotypically 'good' freedom fighter faction and so on. The issue was that in all three cases you were a mere lackey, being pushed around, ordered to do this and that. What if you wanted to strike out on your own? Be individual? Be the BOSS?
Thankfully Bethesda listened and eventually introduced the Nuka-world expansion, that allowed the player to take control over a gang of raiders and act as their overboss. Instead of "liberating" settlements for the minutemen, you conquered them for the raiders so the settlers could be squeezed for essentially "protection money", working as little more than land slaves. Now THAT was cool. It just felt tacked-on because the option was not available at the start of the game. Nuka-world was practically only available later on. Indeed, in the beginning of the game, the leader of the 'good' faction, the minutemen, was positioned something like mere 100 meters from the exit of the vault. You were supposed to be set upon the 'good' path right away. I don't like that.
Regarding lack of options:
When I finally got into the institute fully intending to blow it all up, I found out that my missing son (main story), now a middle-aged man, was the leader of the institute. He and the institute were somewhat peaceful, so I engaged in conversation intending to learn more about what happened and their motivations. After a while in the conversation, I realized that the game treated me as an ally of the institute and the dialog ended in them giving me a mission. All dialog options pointed in this same direction. At no point did I say "yes, I will work for the institute". There was an option to denounce them in the beginning, but after that, none.
This felt extremely forced. Just by engaging in conversation caused the game to assume that I ally myself with them and reject the other two factions. All I wanted was more info. So, once the dialog was over, I shot my own son in the head since that seemed the only way to cancel the "ally yourself with the institute" railroaded storybranch. Now Im sure I was supposed to feel moral dilemmas just by talking to the institute (seriously, they are some whack-jobs), but this whole thing missed its mark completely due to the dialog. I ended up going on a rampage and killing most everyone in the institute, eventually blowing up the institute alongside the minutemen (who I ALSO didn't want to ally myself with, but thems the breaks). At least I COULD salvage the situation somewhat, although not in any way I originally intended. I did not want to shoot my son, but it seemed like the only option after the game completely ignored what I actually wanted to do (just say "no").
I think this has been the biggest disconnect with the devs intended storyline and the PC that I have come across.