I have noticed something. Kojima has always written narrative where the main character is always "on the defensive" so to speak. Whether it's Big Boss, Solid Snake, or Raiden, the main one is always being duped to some degree or is finding out some group with tremendous influence.
Take MGS2. You only play as Snake for as long as he remains at a state of great disinformation. For the rest of the narrative, Snake (now an NPC) is with Otakon at the offensive, with greater knowledge and actively going after the Patriots. It's the same situation with MGS5, where you don't play as the real Big Boss for the entire game (except Ground Zero, where he is fooled by XOF and Emerich).

It really tells me how weak of a writer Kojima is.