I don't think the writer from Crysis 2 is involved with Crysis 3 (correct me if I am wrong) and I would be very surprised if the character of Alcatraz plays any important role in the upcoming game. They could go really out and have the suit completely reconstitute Prophet inside the suit.
We'll see when the game is released
This is why we get "butthurt". People like you (no offense) think that just because Alcatraz didn't talk during Crysis 2, he's nothing more than a puppet. Crytek has already stated they didn't have him talk so the player could feel more like they were Alcatraz. Crysis may be a sci-fi game but it is a lot more realistic than you would think. Crytek won't simply make the nanosuit magically bring Prophet back and take over Alcatraz' body.
If anything in Crysis 3 we'll see Alcatraz going crazy from being able to remember another person's (Prophet) life as if he lived it himself.