I think it has been confirmed that Snake will be the only main character in the game, and it also has been confirmed that Snake will make his last "starring" role in this game.
I don't believe he will die in this one, but I would kind of like him to(please don't flame me for that statement).
I <3 Naomi, she was such a strong character that added an extreme amount of emotion in the first one and I probably am most excited to see her again in the fourth.