I don't see the incompatibility as unusual. You can't run an Android based app on a Windows or Linux or Apple computer. Apple II software won't run on any Mac, nor for that matter will Mac OS 9 and earlier software (or OS X software written for the PPC processors) run on a current Mac (or iPad, or windows computer, etc.)
Different processors have different requirements. They also have different strengths, which is why you don't find the same processor in a Mac Pro as in an iPhone, etc. It might be possible to replace the processor and rewire your Mac Pro to accept and run iOS and iOS software, but I don't think you'd be happy with the results.
OTOH, Apple could supply (and charge for) both the iOS and OS X versions of current software in the same package. Then the complaints would come from the people who had an iPad, but not a Mac (or vice versa), and had no use for a second version of the software.
Regards,
Barry