You do realise we're talking about a sci fi styled game with an alien invasion and a super suit that regenerates its occupant? I really doubt that someone coming back from the dead is that implausible.
Not really. Super suit is a story mechanic that KIND OF makes sense, at least in the nanobot fairy magic kind of way, but really, how do you resurrect someone from the dead who has been dead for at least several days and has a bullet in his skull? The story has to at least have some element of plausibility.
I played Crysis 2 but I have no clue at what point Prophet was alive again. I actually remember nothing of that game, however, I assume...
Prophet obviously downloaded his mind into unsuspecting Alcatraz. It's the only plausible way. But, is Alcatraz still Alcatraz or is he now Prophet? Does Alcatraz still exist? Have the two fused to become Alcatraz-Prophet?
Crysis 3 raises tough philosophical questions!