and never the option.

Same with pal in the southwest cave.

Why can't anybody share their reasoning or lay out what has been done and why?

There are a lot of things like FEV use, University point, various people who were replaced and what happens to those who are that could really colour how we see the institute and the things we hear about.

There are so many questions I'd ask given the chance.

At least Maxon lays out his thinking for you at listening point bravo, agree or disagree, you know how he feels.

Doctor Li had similar feelings about the Institute's lack of transparency.
Something worth considering in your evaluation of them while playing.

Still, even if they told me they couldn't talk about it, I wish I could at least pose the questions.

Like the super mutants in the fev lab, I wish I could ask father (or Virgil) what the hell they were thinking.

Could probably sum it up as "experiments, oops".

Yes, with one character I pretty much played the whole institute quest line in hope of getting at least some real answers. Be it through terminals or notes, be it through conversations. I rerolled to an earlier safe when I didn't get any.

There's plenty of answers to be had. The answers are exactly what they appear to be, though, which is what's bothering people as the Institute isn't HIDING the fact they're ruthless to any real great extent.

1. WHY DID YOU DESTROY UNIVERSITY POINT?

Answer: Because we wanted their nuclear technology.

2. WHY DID YOU MAKE SUPER MUTANTS?

Answer: We needed troopers but it didn't work out so went with Synths.

3. WHY DID YOU KILL EVERYONE IN VAULT 111?

Answer: We had what we needed.

Yeah, I agree OP. You finally get there, and Father explains how they're "just trying to help" but those ungrateful surfacers "misunderstood" and now attack them (how ungrateful!)

And I desperately wished I could ask..... how exactly are they "misunderstanding" the kidnappings, the replacing of people with synth dopplegangers, etc? Like that mission where they ask you to take the test seeds to that farm, where they replaced the family head with a synth. Why did they have to do that, to test grow some seeds? Set up your own farm, or get the seeds in via a "trader" who "got them from another region", and just have some non-copy human-synth workers join the farm as a worker to send back data.... all sorts of possibilities that don't involve kidnapping/killing a family patriarch and replacing him with a clone.

Deliberately piss off the people, then act all surprised when they fight back.

Well, the leader of the farm would definitely have more access than some generic random worker you send there. Hell, he might be killed for stealing food if he tried to take samples. And if the institute arrived and asked nicely I am sure they would probably just get shot. They kidnap and replace people before they have to do their work in secret. It is not ideal, but kidnapping is not a goal, it is an unfortunate side effect. For the most part, the institute ignores regular people as much as it can, whereas those same regular people will kill anything they even suspect of being a synth. You walk into diamond city and see some guy getting his head blown off, for no reason other than everyone is paranoid about synths, then you find out that the mayor has been a synth for ages and has done absolutely nothing wrong, he is only there for intel. I would feel safer surrounded by synths than I would surrounded by all the crazy paranoid people who will probably kill me just because they are in a bad mood.

Its not confusing if you stop and realize that the Institute are evil. Yes, the are technologically advanced. Yes, they are clean and polite and superficially civilized. But end of the day, they kidnap, murder and "replace" people. The first two are bad enough, the latter is so unthinkably despicable we really do not even have a word for it in English. They are basically treating all non-Institute people as lab rats. They fail to recognize how cruel, inhumane, and positively evil it is to kidnap people, torture them (apparently to get them to release their memories!?) so as to program their doppelganger, and then dupe whole families, whole communities, indeed the whole Wasteland into believing that one of their Synth abominations is their friend or neighbor!?

I admit, before I was confronted with proof in the Institute, I remained on the fence about them. Maybe there really was some good reason for the Synth doppelgangers . . . maybe there were not so many as the rumors seem to suggest, maybe the people who were replaced were somehow better off?

Having now read most of the terminals in the Institute, and thought about it, I have decided where I stand: The Institute must be destroyed. Its advances must be shared with the Wasteland and its resources distributed to the people. The BoS might be the best candidates to ally with in my goal to do this. Also, my son, Shaun clearly must die, or at least be brought to justice. But in the absence of any kind of jurisprudence or penitentiary system bringing him to justice would seem to equate with death.

Exactly why I do not trust/believe the individual who calls himself my son and exactly why I always destroy him and the rest of his sketchy band of fools. Except for that one save file I created just to get the achievement... which, as soon as that popped, I loaded a prior save and promptly destroyed them.

The BOS don't share technology. They also want to destroy all of the Institute's research.

There's no pro-science enemies of the Institute.

Also, I like to remember the Institute's crimes are almost all its leadership's.

You're kidding yourself if you think the Brotherhood is going to share anything with the wastelanders.

The Commonwealth will tribute recruits, food, and supplies to the Brotherhood in exchange for protection. While the Brotherhood keeps all the goodies for themselves.

I think this is something people keep overlooking or miss the significance of. The Brotherhood's stated goal is to collect and hoard technology to keep it out of the hands of those that would wantonly abuse it, like those that destroyed the world. Here the Institute has some very advanced technology but the BoS hasn't come to add it to their collection. They have deemed it so dangerous that they feel the need to outright destroy it.

My current head canon is the SS sounds the evacuation alarm before blowing up the Institute. This allows many of the scientists (and their families) and synths to escape to the surface. Therefore, at least the knowledge of the Institute' advances in bio-sciences, engineering, advanced systems, etc. will live on and could benefit the Commonwealth in the coming years.