Alex,
Other than size, there is no operational difference in the iFly GPS app for the Mini or the regular iPad. Really, the same is true for a 7" tablet or a 10" tablet on Android. Equal functionality is the goal.
With that said, there will be some UI changes when we introduce the iPhone version and possible a revised Android phone version, simply due to the smaller screen sizes and need for larger and less buttons. I hope this answers your question.