Multitudes of posters insert theories and their own longings into these discussions, but there's no basis for any of it, and the institute just doesn't make any sense, from start to finish. Bethesda you dropped the ball here.
1. Why replace people who already exist with synths. You can't possibly really care if you are the mayor of a freakin baseball field. And that is your top position above ground. Plotwise, it creates the big bad boogeyman, but there's no clear reason for it ever given, ever questioned, and you can't confront Father about it. That's a big problem.
2. Where are all the mutants coming from? I read the terminals and it mentions disposing of them. Not releasing them. And even if you were, why? They complain about how horrible the surface is.... well supermutants are one of a few key reasons. Based on the small FEV lab, I find it hard to believe that this is the true source of all the mutants, but the question remains, what was Father trying to accomplish by the constant tests?
3. Totally contradictory logic towards synths. The institute puts synths above ground, mass produces them, talks to them, etc. But then deny that they have any sort of personhood, free will, or self. Never did anyone at the institute have to provide a reason why these programmed machines constantly were trying to get freedom and escape. I would think programming them to believe they aren't really alive would be rudimentary, and prevent any BS like this. The BoS actually feels the same way. So why make robots that can't be told apart from humans if these robots don't have real minds? The insitute would HAVE TO come to the same conclusion as the BoS, that they are dooming humanity and the world to eventually be a soulless husk filled with algorithms rather than thoughts. So their central activity runs completely contrary to how they think about their own creations.
I love how after the end, the minutemen constantly say things like "I don't know why the institute didn't just stay underground/leave us alone." Yeah dude, NO ONE KNOWS. Cause it was badly written.
I love this game btw, 11/10 for me, because bethesda games aren't on the same scoring scale as other games (except maybe bioware games), But the more I think about what kind of questions I had and how none of it made sense at the end, the more irritating it gets.