*Mild spoilers*
Firstly, I am very disappointed in the story so far. Bethesda could have done more with this than force a player to pick a side. Why not allow to unite them or at least create some form of uneasy peace? Instead they created three factions who are ridiculously fanatical and can't be swayed from hating one another.
I finished the Institute quest line last night. Kept earlier savegames because I want to see all endings. This ending disappointed me though.
Anyway, the G3 synths... in my opinion they're not that different from us humans. Yes, technically they're completely made by humans, but it should be very clear for people to see that they do think, have emotions, morals, just like us. Yes, they're programmed to behave this way, but if they can compute hate and love, despair and courage, is it really that much different from the 'programmed' chemical processes inside our own heads?
During the Institute storyline you're asked to return a synth who became a raider leader and is made an example by Father why letting synths loose in the world is a dangerous thing. But they're not all like that. You meet plenty of synths that behave like normal people, good people. Synths that fight against bad people.
Again, this shows how close to human they are. One synth becomes a raider, another synth becomes a farmer. Why judge all synths because one synth decided to go bad? We don't judge every single human out there when a couple of human raiders do miserable things. And we don't judge the ghouls for their feral cousins' behaviour. I don't, at least.
With that in mind...
Brotherhood:
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Maxson is a scary son of a
, out to kill all mutants, synths and ghouls, whether they're feral or not. I can understand why there's hate for mutants, because a good mutant is hard to find. But they have no right to kill normal ghouls, they're people like you and me. Just... uglier and with long lifespans. It's outright murder.
The hate for synths; even when one of their own turns out to be one, Maxson keeps on spouting his hatred for them, completely disregarding the fact that this particular synth has done so much for the Brotherhood. It's first hand proof that not all synths are to be feared, that they're not all bad.
He's a first class arsehole and although I will be wanting to see the BoS ending, I'd never pick his side.
Also worthy of note is that the BoS weapons dealer has some very dubious work for you. I didn't accept his job offer so I don't know how those missions can play out, but I'm sure nothing good can come of it. But at least Fallout 4's Brotherhood is closer to the Brotherhood I know from the first 2 games: A bunch of tyrants who are only looking after themselves.
But Gotcha!, they sweep the Commonwealth, killing raiders and mutants, thus helping regular people!
That's not strange. They need food to eat and if their actions would make people want to support their cause by donating food then that's a problem solved.
It's a pity though, since there are good people among the Brotherhood. I really liked several of them.
The Institution:
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I don't really know to what extent their actions go. I've gotten little to no proof of them actually kidnapping humans and replacing them with synths.
It's mentioned outside, but in the Institution itself there's no proof to be found, or I somehow missed it.
There is the matter of the FEV lab. I've not found much proof of what was being done down there, but the examples were enough for me, and the experiments were horrible enough to make a scientist run away.
Because of my feelings about G3 synths I feel they shouldn't be kept like slaves. It's clear some of them want to get out, live their own lives. To the Institution they're nothing more than robots, but to me it's clear that they're as close to a real human as anything can be.
I also feel they're being incredibly selfish with keeping themselves underground. They could do so much good in the Commonwealth.
As I've said, I finished this quest line to see how things would play out. Will reload an earlier save, since this is not the faction I want to support.
The Railroad:
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Due to how I feel about G3 synths, I do think these guys are good people... if not way too fanatic. They seem to care more about synths than actual humans and sacrify themselves wherever necessary. I wouldn't sacrifice myself in favour of an unknown synth OR human. It's crazy.
In the end, they mean well. Sure, some synths could become mighty pirates, the scourge of mankind, but others are good people. Again, plenty of examples there.
It remains a fact that there are synths down in the Institution who desperately want to live their own lives, instead of being stuck in an underground base where people use them as slaves. It doesn't feel right to me.
A human can grow up to be good or bad, a synth can go good or bad. There's little difference between us.
I will probably stick with this ending. These guys are not perfect, but to me they definitely feel like the lesser evil here.