I simply do not understand the institute. They immediately claim to not be the bad guys and that they save humanity but never say how.... In what possible way do they help anyone else in the Commonwealth?

What is the point to devoting your life to making a machine as human as possible to the point where they have human DNA if you are still going to demand that they are "just machines". If you want slave labor from machines that will never betray you, why not just use regular robots?

If the Father knew you were his Dad the whole time, why wait 60 years for you to wake up?

I honestly do not understand why the Institute has any interest whatsoever in the Commonwealth now that they have their pure DNA sample.

What is the point of replacing common poor settlers with uber expensive synths?

They just seem like a poorly written and poorly thought out generic cartoon mad scientist faction..... Makes me miss the raging faction arguments as to who would be best for the future of New Vegas.

Humanity already tried to destroy itself. So the only way to "save" it, is to finish the job. No more humans means no more humanity, so we saved the humans from themselves,

- when they say " saving humanity" they refer to " the institute faction " , and what's better for them

- they don't help anyone

- they rely on Synth for top-side scavenging , surveillence & infiltration

- because you can

- you ware stored in vault 111 as a backup in case things go wrong with shawn

- they kidnap people for FEV experiments and infiltration missions - bethesda casually omitted to give u quests that direct you to kidnap people for science experiments , and so u remain with the opinion that the institute is good and shiny

- perfecting the infiltration techniques

- they are poorly designed quest wise but if u read the terminals u get a sense of what's going on ... you just don't have the quests

- ignore him he's trolling

No I'm not. I'm the Director, thats what I'm doing. Thats my master plan.

I suppose that none of the faction really do that much to change lives in the Commonwealth for the better over time..... Even with the Minutemen, you are the only member doing anything..... The "General" title is some kind of sick joke..... Everyone else gives you orders and makes you do ALL of the work and then they say "thanks boss". Empty title.

They don't help the Commonwealth because they think the Commonwealth, as with the rest of the surface world, is beyond saving. The Institute believes that, given the chance, those on the surface will destroy the world all over again because, in spite of the changed environment, their mentality hasn't evolved. People are still driven by materialism, prejudice and irrationality, as you can see with Raiders and mercenaries being so pervasive, as well as prominent factions like the Brotherhood of Steel and the Minutemen (and, not in Fo4, the NCR) repeating history in all the wrong ways, with corruption, authoritarianism and/or petty rivalry bringing them to arms against each other. The Institute's long-term goal is to wait out the inevitable death of the surface world (or, at least, inevitable from their point of view) and repopulate with their own, utopian society (again, from their own point of view). They have no interest in the Commonwealth, they just use its environment and people as fodder for experimentation, so that they can perfect their own knowledge and technology.

Synths aren't very well handled from a logical point of view, though. They probably have very well-developed cognition because they're expected to perform even high-level tasks to a reasonable degree (e.g. conducting research, infiltrating the surface world), and in the future will be expected to provide most, if not all of the labor, leaving the Institute and its descendants only high-level commanding to do. You're right, though, that they're effectively human beings with transmitters stuck into their brains, so it's bizarre as to how the Institute doesn't recognize their status as such. It's likely that they consider synths, just like surface-dwellers, to be just tools to be used and disposed of at will for their own means, which is why they allow themselves to treat them so unethically.

This is getting really close to proper spoilers, but there is a portion of the Institute questline where Father explains his motivations. Long story short, it's just another experiment. He, like the rest of the Institute, was raised to become so far removed from emotions, attachments or anything that could compromise his position as Director, that he decided to treat his own mother/father as just another opportunity for research (though this isn't entirely accurate, as he does have some bias towards you).

The Institute believe in advancement of the human race through the most technological progress they can muster, regardless if its a good idea or not. Making a human like synth isnt really a good idea, causes all sorts of rebellion and unrest in your population, but then they made them for exactly one reason: Creating the most advanced robot they can dream of. This is why they are filling the standard villain role, despite them being joinable. Nearly every villain in a story has flawed plans, going by Fallout the Enclave want to create a genocide of the mutated populace, which would result in them being severely underpopulated and most likely be bombed from whatever rebuilt air power to turn them into dust so they can't spread their toxic filth. The Legion wants to conquer the entire wasteland based on sheer physical strength, which doesn't work well at all when you have knives and football loricas versus automatic firearms, and thats just the NCR.

The Institute builds the things they build because they see it as their duty to apply their technological knowledge in the most advanced forms that they can possibly make. Its over engineering and perfectionism that would soon end in fatal results.

They also fill the mad scientist seeking dangerous technology trope to go with black armoured supremacists seeking genocide and a rebuilt empire seeking brutal world conquest. Lots of the stock villains that you would find in post-apocalyptic works. Doesn't mean they're unoriginal, but that a lot of their mustache-twirling comes from needing a clearly defined enemy in a world like this.

Why are you assuming they want to help the Commonwealth? To them the Commonwealth is doomed. What they mean by wanting to help humanity is that they are the best hope for humanity. In many ways they are right.

To build upon the lore in FO3?

Pretty much of all this is explained in-game, but:

Just weak Informations from Bethesda. That is the biggest Problem with the Institute.