Well, the Enclave were the good guys at the end of Fallout 3. The Brotherhood were foolish idealists who decided to attack another group, who shared their cause. Simply because they wanted to be the ones to save the world.
This all depends on your idea of "good guys." Their plan in FO3 was a smaller more half baked version of their plan in FO2. FO2 their plan was to use a modded airborn mariposa FEV to kill all mutations IE: Everyone and everything not given an inoculation to their FEV. It was to be sent into the Jet stream and taken around the world.
Spoiler one way to get off the rig is to convince one of the Enclave scientists to give you and the Vault 13 and Arroyo prisoners an inoculation against the FEV. He then lets the FEV out into the Rig, killing all not in Power Armour.
FO3 their plan is to infect project purity with a water born version of FEV. I called this plan half baked because it all came down to
"Gosh, I hope the Lone Wanderer helps us". With the original ending their plan would have infected all the water in the Tidal basin and water in the rivers as well. With Broken Steel their plan becomes even more lame, the water is now dispensed by the BoS by drums. The water in the Basin and Rivers was not cleaned only the water in project purity is clean. Point is I am sure the Enclave in FO3 would have an inoculation against their modded FEV they used in FO3. Their goals would be much the same. Only thoses they see fit to live like FO2 mutations include everyone and everything in the wasteland not inoculated.
So unless you are on their good side they are your enemy in the end. They don't want to save every wastelander only those pure enough. Both Enclave on the West Coast and East Coast have been destroyed. I don't want them back, so my money is on the BoS.
All that being said there are three BoS groups. Original West Coast BoS, Midwestern BoS and Eastern BoS under Lyons. West BoS don't share and they don't help, they have no intrest in ruling or running anything. Midwest BoS do help but they will kill anyone and anything that does not give into their demands, still not interested in running anything. BoS in East, are helpful but don't have the numbers to do anything, and the Enclave could have killed them easy but for some reason did not.
I would side with Midwestern BoS, they have the numbers to get things done and they don't care if a few wastelanders die, they have Labour camps and use prisoners to transport radioactive cargo (under the watchful eyes of power armourd guards.) Western BoS because they have the tech and are just the original bad asses that started it all. I would not pick Eastern BoS, to few in numbers and would get their asses handed to them.