What? Sorry, but I can't stand the BoS. Big guns and armor and not much else. Their whole philosophy is terrible and, to me they are nothing but a bunch of militaristic thugs that offer nothing to the dynamic of the game but conflict. It's just my opinion.
I prefer anyone besides them.
I am not a huge supporter of the Institute, but, my point is that, the Institute is in no danger from the BoS. They have already been infiltrated and can be again, easily.
I personally prefer the MM and the RR, since they, at least have goals outside of simply conquering and destroying.
You cannot honestly tell me you believe that the BoS has the Commonwealth's best interests at heart. They always do the same thing. Come in. Invade. Take all the resources (and anything else they want) and then move on. It is their modus operandi and has been in all of the games.
Perhaps it is the xenophobic attitude that no-one except themselves deserve to exist and that they automatically are entitled to everything, and if you do not give it to them, they will take it.
Sorry, but I do not believe that the Supers are evil, nor the ghouls (including the ferals). They are the product of what we as humans created and now we have to deal with them and all the other mutated things that exist now. I also do not believe that synths are evil and deserve to be destroyed.
I suppose it is biased to support one team over the other. The question was, who would win if my character had not existed. The Institute. The MM are simply too weak, the RR too idealistic and the BoS too blind and poorly led. The Institute is organized, hidden and has existed for a long time completely separate from everyone else and has consistently used their abilities and resources prudently and well.
While I do not support the Institute, it is my opinion that they would win out in the long run, without question.
Don't believe me? What about the BoS not even being able to take out a group of ferals (10 maybe?) without the help of a woman that only just got out of a Vault after 200 years. The Minutemen couldn't take care of a rather small group of raiders without help of the same woman? And let's not get started on the Railroad...