Spoiler
In regards to the F.E.V. labs, there were multiple scientists, but when Virgil decided to force a shut-down, there was an error and the virus was leaked, transforming Virgil and the other Scientists. Virgil managed to teleport out, but the other Scientists were neutralized by the Turrets and the Assaultron(s).
If you do the Bunker Hill quest, Father openly admits he's never been to the surface, and staring out over the ruined city of Boston confirms his 'belief' that the surface world is a lost cause, as are the people. And sadly he's not alone in that, as almost all of the Institute's Human population fears the surface world to a level that's almost overwhelming in scale. We're talking about a bunch of people descended from college students and professors who built themselves a high-tech basemant and cowered down there for a few hundred years, and they have no idea of what life really is on the surface, because they live smack dab in the middle of the crappiest place in this crap-sack land.
Thus far, I've yet to find any real evidence either way, but it seems that the Institute was the force behind the collapse of the Commonwealth's first attempt at a provisional government. And Father is most certainly not the messiah but a very naughty boy for what he's done, and what he's allowed others under his watch to do. They are the definition of the phrase, 'The road to hell is paved with good intentions', because they've turned into basically top-tier Raiders while pursuing knowledge for their own survival, and then purely for it's own sake, taking whatever they want at gun-point and dismissing the lives of those not of their group as immaterial. They are to the Gunners what Gunners are to the Raiders and Forged, and it would take a very charismatic leader and a very intensive program of social experiments and adjusting to alter this shared mindset between the Institute Dwellers.
Logically, I can understand, even applaud, the Institute's goals, even some of their actions, but the rest? Razing a farm after an experiment is done and killing everyone who lived there? Forcibly kidnapping people from the surface to replace with Synths purely to test the infiltration programming and using the kidnapped people as guinea-pigs? Sending in armies of Synths to strip whole settlements of every available resource and shooting down anyone who lived there.
With the exception of the Minutemen, and even their claim is dubious for several reasons, not the least of which is their recent history, but the joinable factions are all morally ambiguous at best and downright zealous at worst. Brotherhood of Steal (not a typo) have apparently stripped the Capital Wasteland of the bulk of metal and technological supplies to build their flying fortress after the Enclave base-salvage ran short of building materials and the bulk of their forces are on the Prydwen, leaving only a skeleton crew to keep the peace back home, and Deacon mentions a few times that under Brotherhood rule, the Capital Wasteland has become an oppressive place where the Brotherhood rules like feudal lords, untouchable by the law and controlling the populace with an iron fist.
There's also a troubling undercurrent when you read up between the reign of Lyons and the reign of Maxson in that 'every' leader after Lyons was lost to 'misadventure' or 'ineptness', lending credibility to the theory that members within the Brotherhood who disapproved of Lyon's 'protect the people' angle actively subverted and betrayed the following leaders until they found a suitable puppet/figurehead in the form of the young Maxson. And let's be honest, his predecessors were all seasoned veterans in their own right, for them to just up and die and/or fall victim to malfunctioning equipment or obvious ambushes seems ... odd to me?
Also the fact that the Brotherhood, in it's current incarnation, has drifted so far from the original reason of their creation, to defend the populace against a cruel, ammoral government and powerful super-corporations that practiced inhumane experiments on the populace and recklessly wielded technology and science without a care for the side-effects that it's not funny. They have become a toxic imitation of the very entities their beloved Founder so despised ...
The Railroad is ... on the one hand, they are freeing sentient beings, and people will say that Synths go rogue, but Samwise in the Bog contests this best, by asking how many times a Human has just turned homicidal for no reason when talking about how his people were ejected from Diamond City. On the other hand, as much due to the loss of the Switchboard as Desdemona's obsession with freeing Synths at all costs, the Railroad has stopped helping people who are kidnapped or enslaved.
It's also unclear if the Railroad was founded to protect the Synths, or adopted that cause after encountering a 'rogue' Synth wandering the Wasteland.
It's also unclear if the Railroad was first contacted by Rogue Synths who had escaped the Institute (which further lends credibility to the concept that Synths are independent, self-aware entities on-par with Humans in mental/emotional capacity) who were seeking refuge, or if the Railroad actively tried to save the Rogue Synths, believing them to be normal humans at first before discovering the truth after saving the 'slaves'.
I applaud Bethesda for the depth of their plots in this game even as I curse them for the feels I suffer when I turn against one faction or another to progress the story. Every faction, even the Institute, has valid reasons for their actions, at least to their own form of thinking, and has goals outside of Crush-Kill-Destroy-Swag.