Apple's hands are tied by decisions made long ago re display layout. Because elements are positioned absolutely and not via a layout manager, they can't go with an intemdiate resolution - they're tied to either 1024x768 or 2x that.
But the latest iOS has some kind of layout manager anyway. Perhaps the iOS device range is going to become even more fragmented in the future. I'm not sure that's a great idea from anybody's perspective, but as long as people keep buying the devices, developers will continue to suck it up.
There is no comparable solution if you simply increase the PPI of the iPad Mini by 50%. It's either 1x pixels or 4x pixels, there is no middle ground.
The iPhone 5 lengthens the screen by 176 pixels in 1 direction, leaving an old style layout with 88 pixels of banding (a bit over 6mm) on each edge.
For Apple to run with a sreen resolution similar to the Nexus, say 1200 x 900, we'd have banding of 88 and 66 pixels along each long and short side respectively, so it wouldn't be too bad.