I would love to be able to program my Phantom to head up into the sky and go and collect the imagery I want from predefined points, or to follow a predefined track to create a an aerial imagery mosaic. Doing it by hand is nigh-on impossible, although it hasn't stopped me trying.
Unfortunately I think it will be a while. DJI sell [or did] the Wookong-M, which has waypoint functionality, for about USD1400, so clearly this is quite possible. There may be memory or programming issues with the Naza-M which limit the number of possible waypoints. We know the Naza-M stores at least one for RTH functions. If it didn't, I would have lost mine at least three times.
But apart from the commercial aspect for DJI, this is also bound up with the whole crazy debate about 'drones' and UAVs generally. If you can program waypoints into the Phantom, it moves away from being a remote-controlled model helicopter to something a bit different. In Australia, where I live, the government department responsible for aviation has taken the pragmatic decision that a remote-controlled model aircraft [not requiring certification or licensing] is one that is in visual range of the person flying it, and it is otherwise a UAV [which requires certification]. That leaves most FPV fans rather outside the law, since even a good pair of binoculars is going to have trouble seeing my Phantom at any more than 300 metres away under ideal seeing conditions. But if you programmed a set of waypoints, and allowed the aircraft to progress to them, clearly it no longer meets the convenient definition of an RC model aircraft.
The Arducopter project can already do waypoints, and it might be possible in the next couple of years to do something with a customised Phantom ground element to get it to navigate through a set of waypoints, but I suspect DJI won't want to take their consumer product in that direction.