It's because Fallout 4 is more a shooter then a real Roleplaygame. The only good Thing is, that you can blow up the Institute and save the Humans and Synths in it.
Indeed, just today decided, my game hereby ends, when I found my son. It's the best moment for satisfactory end, I can get in F4 apparently. I've chosen to avoid bad taste of one of available artifical, illogical, cheap "hard choice" defeats. Why to spoil the gameplay with such ending. The situation just beg for a good diplomat, a mediator, who can bind all factions into some powerful alliance, better or worse, or at least to make some balanced truce dending on his skills/deeds/decisions. It could, hell, it should be difficult, to achieve an optimum, but doable. But no. Let's force the stupid conflict instead. Give no chance to reason anyone to anything while logically there are perfectly logical non-violent solutions with synergistic win-win output. Really disappointing as for role playing - shallow. So, I ended by finding my son and I think, I'll rest from F4 till they do something about.
I didn't need to get to know the Institute before I blew it off the map. Once I found out that it was the Institute that sent Kellogg to kill my wife and kidnap my baby that is ALL I needed to know about them. Then once I talked to my son, Father, and got all the condescending, self serving answers to include "Collateral damage" when asked about my wife, his mother. I shot the svcker on the spot. I never liked them and in any play through I do they will end up exactly the same way, a mushroom cloud.
I never liked the BoS, they no better then the Institute. The RR is ok but their focus is too narrow minded for my taste. Even the MM are broken, they can not seem to do anything without me doing it for them. So I do not agree that I end up liking them all. That is the problem I have with the story I ended up not liking any of them and by the end I really could care less about the entire Commonwealth, I wanted to find some super nuke and finish the entire place off. All except for Magnolia of course, her I would take with me before setting the timer