They're really trying to set BB as a villain and it will never work. After mgs3, PW and Mgs4 it's impossible to hate BB, He has all the motives to do what he did, and if we analyze it, Snake is the "villain", even if he doesn't even know it. He's been fighting against the opponents of the Patriots.
People keep saying he will be a villain, even Kojima, but I just don't see how. At best, he's a guy with good intentions but gets blinded by revenge and ends up letting things escape his control. Same could be said about Drake, Max Payne, Wolverine, and so many others. Miller said he was a monster in the early games, but that will be retconned to hell.
After Mgs4 it's impossible to look at him as a villain, in the most conventional way (a guy who's in it just for money or world domination or just plain crazy who wants to see the world burn). He might have taken a wrong turn somewhere down the road, but his intentions are good. Snake too had good intentions and yet was manipulated throughout the entire franchise and thanks to his efforts the patriots were able to remain in power for so long. He's he to blame? I don't think so.
Maybe the real answer is that like in the AC franchise, there are no real "heroes and villains". Everything is grey. It would be jarring to turn big boss from a hero, to a despicable villain, to a sympathetic old man again.
Sorry for the rant.