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Personally I think the death of Lyons and Sarah probably had a bit of an effect on the kid. He idolized Sarah. If you listen to his dialogue he has quite a strong conviction that he needs to help the people of the commonwealth, it is just in a somewhat more militant way then Lyons. Being thrust into a leadership role at such an early age probably wasn't the best for him either.
The Brotherhood of the Capital wasteland had gone rogue, and Elder Lyons was going against the mission of the Brotherhood in order to help the Capital wastelanders. The Outcasts were upholding the original mission of the Brotherhood.
The Brotherhood of the Commonwealth are xenophobic technophiles, which is pretty much exactly what the Brotherhood is supposed to be. They're not as aggressive or zealous as the Enclave with their "restore purity" mantra, but they do look down on wastelanders, and only look out for their own.
And it's not about them being moraly ambiguous for the sake of ambiguity. BoS was created by people who abandoned they duty in the time of war because they were horrified by what can an unchecked scientific progress lead to. And after that it was an endless fight for survival in the hostile world. The philosophy of Maxson's Brotherhood makes sense, it is what you can expect an organisation like that to have. And the philosophy of Lyons' brotherhood doesn't make any ♥♥♥♥♥♥♥♥ sense at all.
Still, they usually aren't genocidal, either. Fallout 4's Brotherhood is similar to the Enclave in that regard. I don't remember them being strongly anti-anything in Fallout 1 or 2.
These are just my guesses
1) Death of Lyons, brotherhood has always had a strong chain of command. How many were only following orders under Lyons we will never know.
2) Constant loss of personal in conflict, first against the enclave and continuing against the supermutants.
3) Reintegration of the outcasts, who presumably suffered less as they were not as proactive
4) Communication with the west re-established, they know that the west has fundamentally collapsed.
5) Maxsons leadership as discussed above
According to terminals within Boston airport and The Pydwen. After both Lyons died, the father and the daugher. Chain of command blewup. It was mentioned that before Maxon took over, the BOS in the Capitol wastland has a bunch of ineffective Elders.
Thus BOS in Fallout 3 became weaker over time, once Maxon took over he overhauled the BOS and brokered a truce with the Outcast and thus the two factions became one.
As for 2 and 4, personal loss for the BOS in Capitol wasteland isn't reported in any way, nor have they established contact with their Western counterparts.
2 was an speculation based upon what I saw in Fallout 3, as they seemed to have manpower issues. That and what we know about the fate of Sarah as well as what little we know about Arthur and Shepard. Speculation in the end.
4 was based on something I heard about Maxson being confirmed by the elders, as I cannot find the evidence of this it is best to be dismissed until I do :)