Vamp suddenly become nanomachine infused creature, and they cancelled his abilities. As for Big Boss. Well i know they did the best to explain how he wasn't really evil. They just went overboard, since brainwashing and mass murder is wrong.
Vamp didn't suddenly "become a nanomachine infused creature", he was from the moment we saw him in MGS2, we just didn't know it was nanomachines or other technology letting him do many of the things he did.
Big Boss? They've gone to great lengths to make him a sympathetic character, but there's also some key information we're still waiting on from Phantom Pain (and possibly beyond) that turns him into the man who wanted to nuke the world from Outer Heaven from Metal Gear 1.