I had it spoiled earlier, but I guessed the body double from the very beginning. People here on GAF were calling out the "Medic is actually who you play as" since the trailers were coming out. There are so many obvious hints to it throughout that it wouldn't have been a surprise even if I didn't get it spoiled.
That said, it explains his different personality.
But WHY? Why put a body double in the game? Why play as random guy #54352354? It's such a weird plot twist. I'm not even upset about it, it's just such a bizarre creative choice to make. However, it does kind of ruin any trace of a Big Boss downfall story that this game was supposed to tell.
And the trailers flat out lied. The whole premise of this game was Big Boss' fall from grace, his explicit fall from grace rather than the implied fall we kept getting, and the story never really goes there. The Eli plot thread is left totally unresolved, as well - what is he going to do with Sahelanthropus and the other strain? He just vanishes after that.