We play the prologue as Big Boss and the rest of the game as the "copy". Remember MGS2?
The issue I have with that theory is that Psycho Mantis' power wouldn't work like that on someone that isn't Big Boss. Only him have the memories of Volgin, Ocelot and of the Boss's horse. There could be some bullshit about memories being passed on throught the cloning but by that time in the game the clones of the Les Enfants Terribles project are also about 11-12 yo so they can't be like Big Boss yet. And why would a random guy they are using by putting him in a coma and dressing him as Big Boss would have those memories?
The artificial arm/robot arm is kinda weird since he doesn't have it in MGS4 but they had rebuilt his body anyway.
'Ishmael' is probably a hallucination.
This is what Evilore kinda proved earlier in the thread. The face under the bandages is probably going to be a real shocker, though.