That's probably why Bethesda kept bringing up 'hints' and 'points' about the Institute being evil (like making and releasing FEV mutants to the surface for no valid reason) when all they amounted to was being xenophobic isolationists who hate and fear the surface due to not wanting to understand it (almost like Vault City except more pretentious about it).
I think the Institute was actually the victim of rewrites since I can tell someone had a very clear vision of them being comically evil superscientists and someone else had the view of them just being ignorant of the rights of Synths as well as deluded about the surface world's chances to survive. They were then shoved together so it's a more complicated situation but more complicated does not = better.
This person clearly hasn't played FO2. The Enclave considers everyone who hasn't lived a Vault their whole life to be a mutant; and even then, they used residents of Vault 13 and other Vaults as test subjects.
Yeah, it's important to understand the Enclave views Wastelanders as Orcs. They're mutants, FILTHY MUTANTS!
Someone should call Magneto.
From my experience trying to make a grammar checker and trying to write a story, it is easier to give advice how not to do something. Take for example FO:NV and Skyrim. Both have a civil war as a major plot point. People praised the conflict in Skyrim for being morally ambiguous and complain about Legion being too blatantly evil. Before we continue, I'll say that I think that the Legion suppose to be evil and the cut-content isn't going to make them somehow morally ambiguous. The thing is the civil war is pretty unimportant to the main quest in Skyrim (the civil war is only relevant to the main quest at exactly two points in the game.) while the civil war in FO:NV is the main plot.
Actually, I'd go one step further and say the Dragonborn is encouraged to think the Civil War is stupid and a pointless waste of lives (like many RL wars) given the Thalmor directly are stated to be trying to keep it going while the Greybeards also state it's a tragedy rather than a triumph. I agree, though, Caesar's Legion is meant to be the "bad Karma" option but it has the benefit of being able to clearly articulate its goals.
I believe the main source of moral ambiguity in FO:NV is the choice between the NCR, House, and Yes man. Caesar's Legion justifies the NCR's imperialistic occupation. Mr. House is only able to have a truce with the NCR because of the looming threat of Caesar's Legion.
Permanent peace in Mister House's home is only possible after the Legion is defeated, of course. Sadly, the truce between NCR and House is dummied out.
The most important part is how it seems like neither party can talk it over. With Skyrim, the main issue is Talos worship. After saving the world (an infinitely more important quest but just as unmotivated as the civil war), the Dovahkiin should have wield at least the same amount of influence as Ulfric Stormcloak. Or the Dovahkiin could just tell the elves to fuck off; because by fulfilling the Dragonborn prophecy, he essentially proved Talos' divinity. The game should have just ended after defeating Alduin. Also, you can't just kill Ulfric Stormcloak because that is too fun.
Actually, it's a bit more complicated than that since everybody believes in Talos' divinity. The question of renouncing Talos was never an issue of someone actually thinking he wasn't a god. Like one human being in the world actually believes the Thalmor and worships the Eight in private. The issue is it was forced on them at knifepoint.
I also see a truce between the parties as the ideal outcome and the lack of permanent one a tragedy which shouldn't have needed o happen.
BTW: The only reason anyone sides with the Institute is to please the Sole Survivor's son.
Actually, my opinion is Shaun is complete scum and my Sole Survivor felt like his son made his skin crawl. However, I sided with the Institute because I felt it was a choice between them or the BOS with the Minutemen or Railroad not feeling they could stand against them. The Institute had children in it and I had to do my best to save a remnant of civilization, even if their leaders were dickbags.