While the structure of the game will be the same (with The Phantom Pain being much larger in scale), The Phantom Pain will have a different user interface than Ground Zeroes. This was revealed by Kojima in an summarized interview with Famitsu, translated by Siliconera.
This difference in interface probably has to do with the fact that Ground Zeroes is a prologue, so there are some limitations in place in order to let the player get used to the new open world nature of the game. As said before this open world will be very large once the player steps into the Phantom Pain part of the game.
Kojima once again did not want to specify a release date for the game, in stead he said that we’ll have to wait ‘just a little longer’.