I reiterate, I keep trying to see the good in the twist, but the twist is just dumb.
It sacrifices the story to have a M. Night twist. That's all it really does.
It doesn't tell the story of a man impersonating a legend. That would have been interesting. Maybe having Big Boss fail at moments, to show that he isn't quite up to it. But there's no indication of "You've gotten slower" or Venom Snake having made a mistake that Big Boss wouldn't. He does a perfect job at being a doppelgänger.
So what is the point? You're not, as I just said, telling the story of a man impersonating a legend; the character might as well be Big Boss, if you consider how he acts and how he's viewed. And to have the twist you skip out on developing Big Boss as a character. We see the downfall of a body double. That isn't inherently a bad thing, but where does his downfall lead him? To creating MG1's Outer Heaven. And where does Big Boss' lack of a discernible downfall (outside of letting Zero and Ocelot create a doppelgänger for him) lead him? To creating MG2's Outer Heaven.
What?
It isn't even smartly done. It's a twist that relies on outright lying to the player, and specifically about only the elements that would make the twist obvious. "Snake was Ishmael all along", "But Ishmael has no facial hair", "Fuck you".
Then, of course, the twist makes even murkier the Metal Gear canon. Really nothing is off limits or sacred any more. MGSV leads to pretty big retcons to MG1, and that domino effect will permeate through the series as a constant cycle if it was ever allowed to continue, everything straying more and more away from what was said to happen each time.
Kojima needs an editor.