Unfortunately, the iPhone SDK is hard-coded to the existing screen size in a lot of ways. For example, most apps contain a Default.png that is displayed while the app is loading, which is exactly 320x480 pixels in size.
It's just a matter of time before Apple releases an iPhone-like device with a different screen size, but when they do, it will be a painful transition.
It could be argued that the introduction of the new device would be the perfect opportunity. Having resolution-independent apps isn't going to help when the physical size of the screen changes. I think the UI changes going from a 3.5" screen to a 7-9" screen are going to be bigger than the changes to increase pixel density on the same size screen.