OmniGroup found a way to effectively get upgrade pricing with the App Store, but it requires your app have two modes: Regular mode, and an in-app purchase to Pro mode. With that setup, you can offer discounts for the IAP to previous customers (basically, by having 2 IAPs that unlock the same functionality, but you only present one to the user). So your repeat customers still need to pay full price for the Regular edition but their Pro upgrade is cheap (or free).

Of course, most apps don't really split into Regular and Pro very well, so this solution won't work for a lot of people.