The main quest is actually pretty much garbage. The Institute as a faction makes no sense at all. The Railroad makes even less sense. The BoS does at least make sense but they're an unpleasant bunch of assholes who I'd never want to win. And the Minutemen are just a failover faction in case you somehow screw up everything else.

Do you know what I had to do for (SPOILER)the battle of Bunker Hill, for instance? I executed the Synth Courser when we first arrived, since I am Railroading. Every faction was non-hostile to me at this point - even if I attacked them. I killed every single BoS and Institute rep with my combat knife, without making anyone hostile. Paladins took 3-4 backstabs, never caring at all, until they were dead.

I made it inside - the Railroad is non-hostile of course, but their machine gun turrets are still hostile to me so I HAVE to kill my own side's turrets, to walk by. I got inside, and learned that my entire objective was literally just walk all the way in to quest-tag the synths (aka do literally nothing but walk into the room) and walk all the way back out, again with no one firing at me.

This is mandatory main-quest event. I could actually probably keep listening utter nonsense interactions and plot holes from even just this one, but I think you get the picture.