Remember when they said that the voiced protagonist would allow them to tell a better story? That... doesn't seem to have happened. Then again, the idea that a voiced protagonist will allow you to tell a better story is nonsense. It can allow you to tell the story better, but it doesn't make the story itself any better.

Hard to know, all the Institute scientists who made that decision are long dead. It is possible that the old Directors were even more hateful than Shaun's regime.

As far as FEV goes, I am pretty sure that the red liquid in Robotics department is actually a variation of FEV, thus the final step of creating a g3 Synth.

I am not sure if the Institute even has a real goal: they are just remnants of CIT who live their lives in pursuing scientific endeavors. Most of what they do above the ground is related to survival, taking care the wastelandes don't become a threat or random scientific experiments.

Do they need to give any more reasons though? The Institute is already the most chosen faction.

They could have used terminals and the like, as they often did. I think it is more likely that a lot of planned stuff was cut, like it always gets.

Well it's clear from the terminals and other documentation that the cryostasis experament was never intended to last forever: the purpose of it was to see what happens when it FAILS. As such, it may be that in order to keep the backup's stasis pod operational, they had to leave the others offline, because otherwise there simply wouldn't have been enough cryo-stabilization gas or whatever to keep the one pod operational.

My entirely fanon, non-canon ideas are this:

1. Vault 111 had its population killed by the Institute because it was resource strapped and they needed the nuclear reactor energy of Vault 111 in order to provide them power for their experiments and expansion. They only left enough power for Vault 111 to maintain the Sole Survivor and his wife who were to be kept on ice until problems were resolved.

2. They replace people about the Commonwealth out of paranoia and fear for their lives. The Institute really does think the Commonwealth is a huge danger to them and a bunch of savages who are always plotting against them. They thus send Synths to constantly monitor and keep them under surveilance as well as sabotage any anti-Institute efforts against them.

3. The release of the Super Mutants on the Commonwealth by the previous Director is to keep the Commonwealth divided and weak so they don't have to fear any retaliation. The Institute is very paranoid about being murdered by surface-dwellers.

4. Father kept the FEV experiments going because he was hoping to be able to cure his cancer with them. He was actually considering turning his father/mother over to Virgil in order to see if that would help him with it. When Virgil departed, Father gave up on it and decided to reconnect with his parent and Synth child instead.

Note 4# is monstrously selfish and evil but backed up by the terminals.

Shaun explicitly tells you that their goals are to basically stay underground forever, building a new life for themselves away from the broken and destroyed surface they see no hope in.

we were the backup... likely perhaps the least tainted of everyone in the vault chambers aside from shaun. But who really knows?

but it makes an interesting story. kidnap the child, spare only one parent. then wake that parent up when the child is old and grey and see what that parent does?