Major Spoilers ahead

I have finished the game with the brotherhood ending, wanted it to be with the minutemen ( trouble finding a way ) but anyways here's what I think about the 2 factions and the other ones.

Minutemen - They started out weak and ended up strong. In all of the factions, only the minutemen care about the people. Food , water, power , shelter, defense and so on. No other faction does this for the settlers. You can also see minutemen patrolling around the commonwealth to fight against the baddies, super mutants etc. Even if you have setup a lot of settlements in the commonwealth , it is not enough to fight against other groups outside the commonwealth. And this is why I think the brotherhood partnership is ideal.

Brotherhood - We know that all they care about is technology and military power but if you observe the random events in the game. They are the 2nd faction that fights against your enemies, mutants , animals, raiders etc. Risking their lives to fight the bad guys , that explains the numerous vertibird crashes. Still they are eliminating the hostile threats in the wasteland.

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Now the baddies

Railroad - Small group. They only care about synths. I think even Desdemona or almost all of the RR are synths. There are so many settlers in the commonwealth that need help but they don't even bother helping them. In fact I recalled one of the options to let the railroad join the minutemen, side with minutemen or railroad.

Institute - Killed your wife, cloned your son's DNA , experiments, responsible for the deaths of the people in the commonwealth. I don't think all of the institute is bad. Just a few departments , advance robotics and so on, anything that deals with the creation of synths. Their biggest mistake was making synths when it fact they are perfectly capable of just creating ordinary less advanced robots to do their work. And maybe do something like increase their population hehe.

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Beyond the commonwealth

This is why I think Minutemen + Brotherhood teaming up is good for both of them. With so many threats from the other us states, ex NCR, or maybe even future countries. They have the best chance in defending the people of the commonwealth.

The Railroad doesn't help people in the Commonwealth because the Institute is actively hunting them down. Deacon mentions while he wants to help people, the Railroad's family members are targeted by the Institute unless they keep themselves hidden. Despite this, they're still willing to risk their lives every day to help people who most Wastelanders spit on. I suspect the reason they don't help most Wastelanders is they feel abandoned and resent the racism shown the people they love.

Oh and there's no Synth components in any of the leadership, not even Glory.

The Institute is interesting because they've committed so many atrocities but if you find the right terminals, you find out they used to be helping the Commonwealth by sharing technology and aid (why so many laser rifles and other weapons are around society). Then the Commonwealth turned on them and blamed them for the failure of the Commonwealth Provisional Government.

Which led the Institute to flee underground and declare the surface was beyond salvation.

Great reply. Ive done all the endings but saved the railroad for last so I could continue the game with them after the ending. I liked what they stood for over everyone else.

There is no "good" or "bad" - everytime youre deep into a faction, youre presented with their honest intentions (yes, even the institute) then the drawbacks they bring (which they either dont notice or consider a nessicary evil of sorts)

I think theres just a "grey line" between them all this time over.

Like..

Railroad - they will kill humans for a synth, even though its humanity (for synths) theyre fighting for.. They have a "youre with us or against us" ideal. I.e; if you hate synths and they achieved a decent commonwealth standing they may elimenate these people

Brotherhood- believes they are fighting the institute for a good cause when in reality, theyre the definition of pre-war military; they waste resources they cant replenish, take from other people, are very dictoral, resort to killing for mere "loose ends"

Institute - believes they are humanities best hope, even though theyre basically the embodiment of pre-war scientists.. Sure, they have good intentions, what they make is genius.. But what happens when they reach the limit of what is thought of as "enough"? They start testing with FEV, pushing their luck out of curiosity. They think they can controll science but as apparent pre-war.. This will catch up to them

Minute men - they believe by unifying the commonweath, they can achieve victory. But its very unclear what that victory is.. They mean well, they do well.. But what happens once they unify everyone? They keep building with resources that will get depleted? What then? They have very little plan for the future and if they make it out good. Well, theres nothing saying they wont end up like the railroad, institute or the brotherhood

My first ending was basically BoS and MM. I joined the BoS and did their ending, but the MM were left alone (weren't killed like the other factions) so the MM were still around. Best ending in general if you are someone living in the wasteland ... well other than that big boom to finish off the Institute.

But who taught the BoS pilots anyway? FO4 shows us what would have happened in Skyrim if Dragons exploded when they fly into things.