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The Institute's attitude towards humanity is focused on its survival and prosperity as a species, not any particular population of specific humans other than itself, and after past events they decided the surface of the Commonwealth was a lost cause.
Of the four main power groups in the Commonwealth I view the Institute as the most evil, closely followed by the neo nazi BOS, with the Railroad and the Minutemen not even being in the same ballpark. Resource wise the Institute probably has the most resources. It is well within their power to make the Commonwealth a much more pleasant world.
They could clean up the water, use their gen 1's and 2's to drive off or destroy the various raider and gunner bands, re-establish commerce, and generally vastly improve the living standards of honest people who now wallow in their own filth.
Instead they write off all of humanity outside their little fiefdom as being beyond help. Instead of helping them they make their lives even more miserable. That's why, in my last playthrough, when I tried to talk "Father" out of his order to assasinate the leadership of the Railroad, and he refused to talk about it, I killed the cold hearted bastard myself.
Dr. Li is a nuclear physicist specialising in fusion power, which is why she was able to fix Liberty Prime in Fallout 3 and F4. It also explains her position as head of advanced systems and the "Phase 3" power project.
I may be wrong, but I seem to recall Dr. Zimmer (from the Insitute) making some snide comment about the science group as "not being able to clean up their own water"....or words to that effect. Evidently meaning he saw no great difficulty in doing just that.
Sure, they scavenge for materials and need to supplement their power supply (most likely from the numerous functional and readily accessible pre-war sources, which isn't stealing from anyone) until they complete development of their reactor, but they're the same as the other Commonwealth settlements in that. General kidnapping and murder aren't notably high (compare activities in Goodneighbour or Diamond City), and there's a grand total of one leader who gets replaced (and he kicked out the ghouls before the Institute replaced him; he was of no use to them for replacement until after he became mayor).
They tried to help previously. Their current position of separation is due to how they got blamed for the CPG massacre, despite almost certainly not being responsible for the outbreak of hostilities (their synth just happened to be the winner). There was a proposal by someone within the Institute to deploy androids (now known as synths) to the surface to maintain order, but it was understandably rejected.
Compare the activities of the Institute as a Commonwealth settlement to the other settlements. Diamond City actively deported a large group of its own citizens and hasn't done squat to help anyone other than itself. Goodneighbour houses hostile triggermen, shares a penchant for drug-dealing with Diamond City, and generally doesn't care who gets hurt inside or outside its walls. Bunker Hill is a little better, possibly due to not having much local activity beyond basic trading, but it still isn't helping anyone beyond its own self-interest.
The "honest people who now wallow in their own filth" aren't the Institute's responsibility to protect, and those people would just be attacking any synths deployed to offer help, even if it were something the Institute chose to do.
Look at what happens if the Institute wins: They become self-reliant for power, deploy a few peaceful, unarmed synths to Diamond City, and post synth units to guard the roads (just as everyone else does). They're marginally more in touch with the surface, and beside that, nothing terrible happens.
Your son, Father knows all about this. It was to him that Virgil appealed time after time for an end to the ghastly experimentation. It was he that refused to end it, time after time. Your son was stolen from you by evil people working for an evil group. Read Kellog's mind and see that, evil as he was, he still couldn't understand why his orders read to kill all the other vault occupants except you.
Your son was solen by evil people and brought up in an evil settlement. It's no wonder he, himself, became evil.
No, the number we see is certainly not the total number; based on what little other evidence is available a few hundred people were taken over the approximately hundred years for which the FEV project was active. A bad number in total, but also a small number when you consider the impact any settlement can have. More people might easily die in Goodneighbour of drug overdoses or triggerman violence.
Yes, disposing of people at Vault 111 was also bad. It was, however, a single incident 60 years ago, and the people in question were already effectively doomed by the way Vault-Tec built the place; with no hope of any release signal, they would have been stuck there until the systems eventually failed after who knows how many centuries and they all die. The Institute of the time didn't help them, and made use of them for its own purposes, but ultimately didn't make their fate any worse. For both Shaun and the Sole Survivor, on the other hand, the outcome was better than if the Institute had done nothing, since they survived instead of dying.
The Sole Survivor's son was saved from death by people in a settlement who wanted to study his DNA, then raised by people in that settlement even when they had no reason to look after him. Had they been genuinely evil, they would have disposed of the infant after they had what they wanted. But the Institute is just another settlement, and while occasional people within it have committed evil acts, most of them are just scientists going about their work. Were it not so, Dr. Li would have found working there abominable long before we ever turned up.
This deed would have been the morally correct thing to do. The Institute chose not to do it, and instead murdered all the people they could have saved. That, the human experimentation, the abductions, slaughters, and looting leave the Institute moral brothers of the raiders and gunners. Most of the population of Germany during World War 2 were unaware of the genocide being carried out by the nazis. But there is no way they could not have known that by invading country after country their nation was responsible for World War 2. Hitler's generals could have assassinated him at any time, but they chose to follow him. The entire nation of Germany was responsible for World War 2. Hitler couldn't have done it without massive support. The same is true of the population of the Institute.
You're also overlooking the fact that the Institute is a settlement of unique individuals, not a monolithic entity that acts with one will. As a settlement it doesn't even have a strict code of behaviour, unlike the Brotherhood of Steel or similar organizations, and we see people within the Institute with different methods and ideals (like Dr Li, Virgil, Liam Binet, Dr Higgs, and Dr Loken). One director ordered the extraneous people of Vault 111 to be terminated, and that director is no longer the leader of the Institute (and is presumably long dead by the time the Sole Survivor emerges from the vault).
The FEV project is responsible for the vast majority of abductions (with just three confirmable abductions outside it), but unknown to the Institute at large, and unlike your comparison, the general population has no idea that anything untoward is taking place; simple hostility between synth patrols and the surface is a mutual thing, and was largely started by the surface dwellers in the first place.
The only "slaughter" that isn't entirely unintentional (the BMI or CPG) or performed on the orders of a leader decades in the past (Vault 111), is conducted by a wasteland native using Institute forces to indulge his psychopathic tendencies (University Point). It's also something that Father (the current leader) recognizes as a problem, and it factors into why he sets Kellogg up for the Sole Survivor.
The idea of looting is just ridiculous; the Institute sends out scavenger teams. That's not something special; almost everyone in the wasteland scavenges in one way or another.