In particular, if your iTunes machine does not have a internet connection, the user messaging/experience could get hairy. Do you copy the non-iPad version to the iPad, yes or no? Do you tell the user, yes or no? Would the typical non-technical user understand what happened? My guess: probably not.
Also, restoring a backup made from an old device to a new device with higher resolution could get complicated, either technically or for the end user.
Other questions:
- what would iTunes show is on your Mac? "You have twitter, but only the 2x resources"?
- testing effort would explode, as one would have to test apps with partial resources.
I think we will at some time get such partial downloads, but for now, copying the whole app keeps things simple.
Simple.
Generally we have a single illustrator file, some export scripts, and push the resulting PDFs through ShrinkIt to minimise file size.
The result is tiny apps that handle all scale factors, can easily be tinted programmatically, and generally match the aesthetic of iOS 7 and 8.
I'd recommend creating all your assets on non-retina sized artboards in Illustrator. We wrote a simple script to export all artboards to separate PDFs, using the name of the artboard as the file name.
I'd highly recommend ShrinkIt for shrinking the Illustrator exported PDFs, as it can reduce the size by as much as a factor of 10.
Also PDFs really lend themselves to being dynamically tinted. You can use the new render mode in iOS 7+ or something like UIImage+Tint to make sure your key colours are all well defined in your code. (It's really nice when a client suddenly decides they want their app to be orange instead of blue, and it's a one-line change without touching a single asset.)