Why would Apple build a distribution channel and then let people upgrade apps outside of it without getting their cut? I think this was obvious for the Omni guys too, they just wanted this problem to get some publicity.
EDIT: The in-between choice would be moving to SaaS (see Adobe), but that's another discussion entirely
In order to do something like that in the App Store, you have to make your next major version listed as a completely separate app ID. Almost no one does this because everyone in the App Store ecosystem expects new version = hit Update All - and the few times I've seen this done, it resulted in nothing but negative App Store reviews.
By not providing anything other than a single purchase price, Apple has not just discouraged the upgrade price model - they've discouraged everything but a one-time flat price or admitting to the customers that they're truly a SaaS model (by forcing the developer to do it as an in-app subscription purchase).
I prefer this simplicity.