OK, yeah, sure. Crysis is not about storycrafting. Arguably, it's not about gameplay either*. But for what it's worth, I'd like to understand how this universe works. Specifically, Prophet.
In Crysis 2, Prophet rescues Alcatraz, puts him in his nanosuit and procedes to kill himself. By the end of the game, Prophet's mind has merged with Alcatraz's body and in Crysis 3, Prophet is completely in control. So much so, that he even sounds like Prophet (even though he should sound like Alcatraz, at least until the nanomachines of his suit were "unlocked" and could transform into anything he wants).
So, my question is: why did Prophet (the real Prophet) kill himself at the beginning of Crysis 2, if we end up at the exact same place as we left him by the end of Crysis 3? I could understand a poorly-handed retcon with Crysis 3 if Alcatraz hadn't been well received... but Crytek was planning this since the very end of Crysis 2. What's the logic behind all these jumping back and forth between bodies and minds?