I really dont consider either of them the basis of the true organization...
In comparison, with the true uneditted versions, what is better?
For the unaware I'll describe the actual organizations..
Western Brotherhood of Steel - Very similar to the Fallout 3 "Outcasts." They are generally only driven by the idea of gaining technology and otherwise have little to no regard for life as an important resource, as the saying goes "Everyone knows how to make another human, but the secrets to making a P-91 Plasma Rifle are all but lost."
They don't take in outsiders for any reason and generally only have interest in technology based on combat/warfare
Eden's Enclave - VERY hell bent on destroying anything and everything "corrupted" by the powers of radiation, generally they kill all radiated beings even humans. Have a very strong and high grasp on technology. Eden's idea of America is to be pure and unradiated in every sense, and even with a virtuous cause then go about it in a violent and immoral way.
I personally would choose Western Brotherhood, technology is the basis of our society now. How many of you wouldn't be able to get along in your job and otherwise if there was no presence of technology? No computers, no phones, no automated tools.
I think that their cause despite their negative attitude to people is an important and possible one. Although with the Enclave their goal is unreasonable in my opinion. For one, it is impossible to defend against radiation if within its presence, despite what Fallout 3 might tell you. Radiation cannot be "Shielded" you cant wear a suit and consider yourself protected, radiation is made up of unstable atoms with electrons that go onto other atoms and make them instable. So in this sense if anything touches the radiation it is going to be instable, even a few seconds in radiation like fallouts can render your organs instable as they dont recognize the changed atoms.
Also, there is no such thing as rad away, you cant drink some fluid and it will recreate your atoms as normal again. It makes no sense scientifically. So with that in mind I think the enclave has a silly idea and should work on creating America to the best that they can without using the silly idea of getting rid of radiation.