If you think about it, The Brotherhood and Mr. House have a lot in common...they both have no interest in conquest, politics....they are both technological visionaries.
Actually it makes more sense for the Brotherhood to work with Mr. House than the NCR....
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About the NCR, I like the soldiers and rangers of the NCR but I don't like their politics, their leadership, and their capitilism. I don't like the fact that people like Alice Mclafferty, the Van Graffs, and Heck Gunderson, become the economic powerhouses of the NCR, and probably have influence in the senate (well maybe not the Van Graffs). Everytime the NCR orders me to kill Mr. House, it just confirms Mr. House's suspicions about Kimball and Oliver.
The good thing about the NCR is they provide stability and security to people living under their flag but the NCR has its own priorities which are conquest and power.
The ineffeciencies of the NCR and its incompetence makes it ineffective to rule beyond the west coast, if it tried under how things are running, it would collapse on itself.
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I don't have sympothy for the Legion, only reason I would side with them was if my character was a sadistic sociopath.
I don't like Caesar....the fact that he portrays himself as a God to be worshipped, his laws, his brutality, his slave army, his mass enslavement of women to be [censored] by any man Caesar chooses for them....
I would rather have the wasteland be a chaotic nightmare than to have entire regions forced upon the Legion's laws. Enslavement is not security.
Caesar tries to entice you to side with him for the sake of security...but as far as I see it, the Legion is doomed either way. Even if it were to succeed to absorb every inch of land out there and absorb every tribe and civilization out there, it will evuentually collapse from within...unsustainable growth.