I don't really want to go into a deep dive here about how evil The Institute truly are as there are countless videos out there about what goes on behind the scenes with them. No, that's a tired topic that I will pass up on. My main frustrations comes from how Bethesda didn't even try to make a grounded morally Grey faction here that does positive and negative actions.
No one knows what exactly The Institute is or what their main goals are. They all have different agendas and they have different divisions, department heads, etc. Each one looks into varying fields and yet there is no central theme about what their end game goals are. I mean even Robert (Mr.) House said that he wanted to go to a planet that wasn't destroyed like Earth was. Caesar wanted to create a New Rome to have his empire at. President Eden wanted to eradicate all the mutations and non Enclave people of the area to start over at Level 1.
I've looked deeply into this topic and I cannot find any at all with what Father wants. We see him look at The Commonwealth with disgust before entering his HQ again and he obviously has not helped The Commonwealth and has actively harmed it and destroyed some settlements along the way too. So that is off the table. Then what really bugs me is the Slavery theme and how it was not needed here. We saw this theme a lot with Fallout 3 and Fallout New Vegas and slavery is barely a thing in The Commonwealth if we factor non Synth beings and saw we didn't need this topic here.
Instead the topic should have been influenced by Fallout 1 with The Master. The Master sought Unity through Humans becoming Super Mutants to evolve and to adapt the harsh conditions of The Wasteland. The Institute could have had the same reasoning by using Synths as new bodies while some choosing to keep their human minds in order to evolve as they'd transfer their minds over effectively. We've seen House do this 200 years earlier, there are Robo-Brains, The Think Tank is more evidence of this, Vault 118, etc, it is possible for brains and bodies to be separated in Fallout and the person can continue living.
Synth bodies can be vehicles as seen with Curie, which was a modified Ms. Nanny bot that has the potential to be born again as a new being. The central theme should have been The Institute believes that evolving through technology is the best way forward and so some believe keeping their minds while transferring over to new bodies is what humanity needs. Others believe that full transfer is required because human nature is fallible and world peace will never exist while it is there and so they become fully machine like as War never changes. Still others will refuse to become machine at all as they believe it is abhorrent to science and they wish to stay 100% organic.
Imagine Mankind Redefined with this topic