Developers, developers, developers
Despite being mostly invisible to end users, iCloud's syncing ability is a much more strategically important product for Apple than the rest of its cloud services: It affords customers the convenience of keeping all their data up-to-date, regardless of where they go, and leads them to buy even more into Apple's ecosystem. That, in turn, creates an ever-increasing incentive for developers to build apps that work exclusively with iOS and OS X, and locks them in by offering cloud storage that is (supposedly) dead simple to use, free, and--conveniently--unavailable on other platforms.
As such, it's a good bet that Apple is well aware of iCloud's limitations and working on ways to improve it. In addition to the inevitable technical challenges that await, the company will have some patching up to do with developers, who are anything but happy at the way the service has worked for them so far. Ultimately, however, iCloud still has plenty of opportunities to catch up with its initial promises and profoundly transform the way we interact with our computers.
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