Apple's answer is to reduce the hole count by making them multifunctional. It proposes removing the need for a separate microphone aperture by making it part of the socket the headphone jack plugs into. This adds only a couple of milllimetres to the socket length - the mic fits behind the tip of the jack plug. The result: "A microphone can be added to a mobile telephone without the need for an external aperture."
While its only a patent and it remains to be seen if, when and how it would be implemented, Apple appears to be considering combining multiple jacks into one smarter jack. It makes sense too. For starters, less holes mean less physical parts to manufacture (and potentially fail) and Apple is already heading down this road with the iPhone 4 which features two microphones and noise cancellation.
The first mic is for phone calls, voice commands and memos. The second mic is for FaceTime calls and for making your calls better.
The other potential direction could take is to use the new port for beamforming -- where the audio input of the two microphones is used as an amiable directional input. Patently Apple thinks this could be advantageous for the iPhone in speakerphone mode or video camera mode when projecting or recording a sound source at some distance from the device.
Apple could even do away with invasive "breach" type ports altogether and convert its audio/microphone ports into surface contact ports that attach via a magnet -- like the popular MagSafe power adapter found on its MacBook Pro notebooks. I just hope that Apple retains backward compatibility with the millions of 3.5mm stereo headsets that are out there, changing to a new jack entirely would alienate too many customers in one fell swoop.