The Phantom Pain will probably explain more of Zero's motives behind Cipher (The Patriots), and it will probably go more in depth about Big Boss and Zero's antagonistic relationship.
While TPP will definitely touch upon Big Boss' relationship with Zero and Skull Face, according to Kojima that's not going to be the main part of the story:http://www.youtube.com/watch?v=JlUxmd7n_j4&t=2m50s
So what is the main event in TPP? Is it going to revolve around Kaz' intentions/revenge? Kojima said that Quiet was the main heroine, don't you think it's odd that he said heroine and not antagonist? Because by the looks of it it seems she is a boss fight and she ends up captured and tortured by Ocelot and Miller. Is Kojima implying that she's an ally and she is going to play an important role in aiding Big Boss?
Can't wait!