I think you overestimate Apple's competence... or, more specifically, the breadth of the fields to which applies.

Apple is very competent at making things for consumers, and not particularly good at working with developers or corporate IT.

I tend to agree that the App Store is being used by Apple as a tool to market more iPhones and not as a way for the iPhone to become a successful software platform for developers. But I think that's more because Apple is flailing to figure out how exactly the App Store should work; remember that it wasn't originally planned to exist at all. Companies need practice at managing developer ecosystems in the same way that individuals need practice at any other skill.

I feel that Apple made the App Store without really predicting or understanding how it would work out. When it turned out to be a great marketing tool for the iPhone but not a very good platform, Apple used the "There's an app for that" slogan. Making the hardware attractive to consumers was the App Store's strongest feature... naturally enough, for a system built by a company that earns alls its money by making hardware attractive to consumers.

When all you have is a hammer, only the nail-shaped parts of your product ever really get done. The rest becomes secondary by fait accompli, not necessarily as part of a master plan.