I guess the BoS, mainly the MWBoS, but in my book, they win by default considering that they're believable to an extent, The Enclave, not so much.
The thing I dislike about developers is that if they put an evil faction in (putting in an evil faction at all deserves critism) they end up giving them 'cool looking armor', causing many players to just ingore how stupid evil they are, and end up loving them because 'They look so KEWL!'.
I guarentee you, that if the Enclave wore football padding and skirts like the Legion, everyone would hate them, and if the Legion in NV had Power Armor everyone would look past their flaws and join them, if Fallout 4 has multiple ambiguous factions that you can help, they better not give any of them kewl armor, and if they do they better give kewl armor to all the factions.
Bull [censored] I love the Legion even if there armour isn't the best I agree with nearly everything that Caesor says
Plus when I hear there Legate saying things like "We shall see how brave you are when nailed to the walls of
Hoover Dam, your body facing west so you may watch your world die."
and the thing he says to you about the NCR finding our teeth at there throats at the battle of Hoover Dam? If someone is going to be that bad ass I'm going to side with them