They just had the perfect oppertunity to make that transition with the change to iPhone OS X 3.0, so that is no excuse.
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.
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.