I'm torn between which side I should take in fighting both the Institute and the Brotherhood of Steel. I've already pretty much decided Elder Maxson has got to go but am open to suggestions why it would be better to take the Minutemen ending where I don't have to annihilate the Boy King. I'm mostly interested in story reasons, though I'm happy to also be informed of any Companion or loot points.

The Railroad is a decent bunch of people and while they don't really have a "plan" for the Wasteland, the Synths are a bunch of slaves and there's a huge number of them in the Institute. Any sense they might be machines went out the window when, IN THE INSTITUTE, one of them thanked me profusely for the privilege of being alive. Once the Institute is destroyed, they can go on to live their lives as normal human beings and spread the knowledge of the place around a bit.

The big advantage of the Railroad ending is, ironically, the Brothehrood of Steel are utterly screwed in retaliation if you pull it off. Because they use stealth and deception, if you blow them up then the Brotherhood of Steel isn't going to retaliate against the Minutemen or their settlements for killing their God Emperor.

In short, the BoS will have no idea who the hell killed them and might have suspicions but the secrecy of the Railroad will protect its members. Plus, nothing prevents the Minutemen from building up the settlements into a nation by staying as Switzerland during this whole affair.

On the other hand, the Railroad absolutely hates the Institute's scientists and Preston wants as few casaulties as possible amongst the human side. Likewise, there's something tremendously satisfying about the prospect of using artillery to wipe the smug "I am the best at everything" grin off the face of the BoS.

If the Minutemen really are to build something like NCR and a new Commonwealth of Allied Settlements then defeating the Brotherhood of Steel is one of the big ways of showing they are the guys in charge. The thing is, I'm not sure, lore-wise they could survive a retaliation by the BoS which isn't done by the scattered angry remnants of the patrols in the Commonwealth.

Which do you recommend?

I am in the same situation and decided to go with the Railroad, after looking at it through my characters eyes.

He is the General of the Minutemen, he wants the BoS out of his territory, and he is certain that he has the man- and firepower to drive them out. But, why go to war and waste the lives of your own soldiers, when you can just send a few spies to reach the same goal?

Royals and politicians may start wars just to prove a point, or to demonstrate their power, but my character is veteran who was pressured into becoming the military governor of a budding nation.

He not only cares about his people, he also is a part of "his" people. It would be his friends and neighbors who had to suffer the losses of any war he starts. And to whom he had to explain why their sons and husbands had to fall to an enemy who never actually attacked one of their settlements.

From a pure gameplay perspective, if you want to destroy the BoS it's safer to go with the Railroad. I took out the Institute with the Minutemen and at the moment the Brotherhood is whining that they weren't the heroes of the hour, but they're not hostile.

Depends, if you like covert ops go with the railroad, if you like fighting with honor go with the minute men. I made a stealth guy just for the railroad and my melee character went with the minute men.

You wind up destroying both the Insititue and BOS anyway so that doesn't matter. I'd recommend minuteman because you ally with the Railroad anyway.