I've known a lot of serviceman in my life. Many of them are honorable, hardworking, and loyal brothers-in-arms; basically guys I would want at my back in a fight. A lot of them are not. Some of them are just plain idiots. I don't think you understand the difference between a soldier and a warrior. The BoS can train as many soldiers as they want, but who knows what those men and women are actually worth in a fight and otherwise.
But I digress. I think it is a little disingenuous to assume that I don't understand the thrust of your argument, at the least. I get that a lot of people think the saving grace of the BoS is their military structure, but if you think that makes them less susceptible to leadership problems, I think you are insane. They are completely at the mercy of their leader, because they are instilled with the discipline to not question orders, which is a recipe for disaster if your commander is incompetent or insane, a fact which can be attested by any number of historical blunders in large scale conflicts. As I said before, leadership problems can do harm to any organization.
Overall, I believe in the capacity of each person. A militia formed by brothers with honor and integrity can form a more powerful group than a bunch of soldiers trained to jump on command. Don't trust that training is going to give the BoS the edge either; people living in the Commonwealth are like settlers on the frontier. Learning basic survival skills and how to shoot a weapon are probably second nature to them at a young age. I think the biggest boon the BoS has is simply all the crap they have. Having access to arms and armor on a massive scale to outfit people is an obvious advantage compared with people who have to use what they scavenge. The BoS are basically just better funded, but if you want to talk about them being superior as a group, that I don't buy. The people who survive in the Commonwealth are more than capable when united as one.