The problem with this game in one example:

I was working with The Railroad, an underground movement attempting to take down the Institute.

The Institute made me their leader after I infiltrated them for the first time.

I thought, okay, now I can go back and relay to the Railroad that I'm now the leader of the Institute. You know, the group that our whole goal is to take down.

You can't. I felt like I was going insane when I walked back to the Railroad base and desperately tried talking to everyone to reveal this critical information about the war I was participating in. In that moment, the veil was lifted. This is not a world, it's a shooting gallery.

What is the point of even having a dialogue system if this very common occurrence that the main quest forces you down creates this level of dissonance due to a lack of options? Why even have factions? Why have dialogue? The game would not be any better or worse than it is now.

Update:
So, revisiting the game now in depth for the first time since it came out, I realize: there IS a whole side section of quests dedicated to exactly what I was talking about but it didn't trigger for me on my first run! This does make me feel less insane and I'm glad the game is more functional now, but it's insane that a bug occured nearly ten years ago and colored my perception of the entire story so strongly.