Kojima says it would have been better to launch both games at once
Speaking with Famitsu magazine, Hideo Kojima talked a bit about the decision to split the upcoming Ground Zeroes and Phantom Pain into two games, and how he would have rather "released it all at once." Kojima hints that Phantom Pain will most likely come out when the PlayStation 4 "becomes more spread out," which implies a larger install base, and thus a larger wait.
He also touched on the fact that during GDC 2013 Konami showed off a Fox Engine demo, leading people to believe that Metal Gear Solid V was already complete -- but that's far from the reality. Since the game will require "much more time," the decision to split Ground Zeroes into its own game was made to to "allow fans to at least play the prologue, ahead of time." Originally Kojima wanted to offer it up as a download-only to keep things cheap, but since "some places don't have the best connectivity," a physical version will be shipped as well.
Finally, Kojima hints that save data from Ground Zeroes will unlock something in Phantom Pain eventually, but there's no hints as to what that may be. So there you have it -- Ground Zeroes became a prequel episode essentially to help soothe the long wait for Phantom Pain.