Brotherood of steel: Ultimate aim, gather technology and use it.
Enclave: restore the United states.
The leaders
Enclave: President Eden: mostly a good leader but flawed in his thinking with regards the FEV.
Autumn as a second in command who appears to genuinly want to restore order.
BoS: Lyons: branded a renegade for wanting to help the people of the waste. once he is gone who will replace him.
other than his daughter, none of the other BoS seem to interested in the plight of the wastelanders.
Also once the purifier is secured whats to stop the rest of the BoS swooping in?
True the Enclave did have to use a large number of nasty methods to secure their objectives but war...war is hell.
further consider the death of your father.
if he had input the code the water would have been activated but autumn would not have put the modified FEV in would he?
your father and him were fighting for the same thing.