Hah. Friendly Enclave. That's rich. You obviously do not understand their mission statement. They think anyone living out in the Wastes is a mutant, and therefore worthy of extermination to make way for a "Pure racE", whereas the BOS are there to catalogue, record, and try to salvage as much Pre-War technology as possible.
Bingo. You would have a massive black hole in the FO Universe if you had nice Enclave. The Enclave and the BoS are similar because they are descendants of people of upper class backgrounds. The Enclave are the descendants of politicians and bureaucrats, the BoS are descendants of military leaders. The Enclave shares the upper class aspirations of a pure society, free from all the moron masses they've plundered and killed. Btw, not very far from real life, you can buy a 1.2 billion share in your own Enclave-esque sanctuary.
http://www.alternet.org/story/147058/
The difference in outlook reflects in their mission. The Enclave wants to eradicate anyone who is not "pure", which means anyone not a member of the BoS, Enclave, or born in a Vault. In FO:III, your character isn't born in a vault, so you'd die too if the Enclave had their way. The BoS is only concerned with technology, and really only with war technology. There are repeated disparaging references to other forms of knowledge in the game, so you can see the military oligarchy mindset.
From the West Coast, the BoS holds more true to the military aristocracy background, not letting in outsiders, (like Lyons), and looting anywhere they can to get their hands on tech. From what the story so far has been surmised, as everyone on this thread commented, this decision ruined the BoS because they found themselves in a war of attrition where they were constantly losing people they could not replenish. How humiliating.
None of that storyline has been confirmed so everyone here is speculating, but we can all speculate. :fallout: