Apple does offer upgrade pricing in the App Store. It's full retail pricing they've obliterated.
When Apple released Logic Pro X as a new $200 app a couple of weeks ago, I immediately thought it finally answered the question as to where Apple stood on the issue of upgrade pricing. It was the first paid/pro Apple app on the App Store to update a full version, and instead of adding a mechanism to the App Store to allow existing users to upgrade at a discount, Apple - like Tweetie 2 back in 2009 - simply released the new version as a separate app and asked anyone and everyone, new and existing customers alike, to (re)pay in full. Only... it wasn't really "in full", was it?
Logic Pro X on the App Store, like Logic Pro 9 on the App Store before it, was substantially cheaper than the full retail version of Logic Pro that used to come in a box. $199 as opposed to $499. Likewise, when Final Cut Pro X first hit the App Store, it's $299 price tag was far, far cheaper than the $1199+ full retail price tag of the Final Cut Pro version that preceded it.
Indeed, the price Apple asks for both Logic Pro and Final Cut Pro is far closer to their previous upgrade pricing tier than anything they ever asked at retail. In other words, if you bought Logic Pro 9 on the App Store at full price and later bought Logic Pro X on the App Store at full price, you essentially paid the same as you once-upon-a-time would have paid to upgrade.
So, it's not that Apple has failed to create a mechanism for upgrade pricing on the App Store at all - it's that they've succeeded in obliterating full retail pricing. Everything is now upgrade-level pricing, all the time, for everyone. No upgrade sales, just "everyday low pricing". It's the mainstreaming of software pricing.
(Not dissimilar, perhaps intentionally, to how Final Cut Pro X and Logic Pro X have evolved in terms of experience and focus as well, alienating power users but empowering mainstream users.)
That might take first-time buyer profit out of developers pockets, and irk existing customers who just hate the idea of new customers getting the same "deal" as they do, but it also simplifies the process on the store side and lowers the barrier to entry for new customers. What remains to be seen if that's ultimately a net positive or negative, and for whom.
There are a ton of arguments many have already made about the continued devaluation of software on the App Store in general, and the consequences thereof, so I won't recapitulate them here, but it very well could be that part of the devaluation, of the mainstreaming, isn't that upgrade pricing has not (yet) been implemented for existing customers, but that it's become the new normal pricing for all customers.
That might be annoying for those of us, developer and customer alike, who grew up in a time before iOS, when upgrade pricing was commonplace. I'm not sure it'll even be a consideration for those growing up now on iOS. It'll just be the way things are.