Simply put, Apple wants fewer holes in its devices. Headphone jack - that's a hole. Microphone - that's a hole. According to a recent patent filing, Apple is looking to consolidate by combining the functionality of the two into one unified jack.
The patent argues that "in addition to using housing real estate, sound input apertures and electrical connectors introduce openings in the housing and breach the barrier that protects components inside the housing." So fewer holes in the device itself, fewer ways for dust and other gunk to find their way inside. It also jibes completely with Apple's obsessively minimalist design ethos. Another potential perk of the two-in-one design would be enhanced voice quality, thanks to the addition of an extra noise-snuffing microphone - what Apple calls "audio beamforming".
Image courtesy of Yutaka Tsutano