Apple knows what it is doing on app upgrade policy
Pietro Montalcino of Macography.net on Apple's app upgrade policy:
What many users these days are doing is to buy apps directly from the developers' website rather than on the App Store, especially if they are purchasing expensive software (Omnifocus is the classic example). In this way users are pretty sure of getting some sort of upgrade discount when the new version of the software is released.
I am pretty sure that Apple knows what's going on here. I am also confident that they are working on a solution, but it'll take time. You see, Apple is known for being laser focused when it comes to products but when it comes to their inner IT systems they are like your average corporation. Vexed interests, relationships with vendors, changes that have to be approved and tested make changing a payment system a painful project. I worked on this stuff for a large part of my career in IT and trust me, development on a payment system is a royal pain.