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iMessage now unifies your Apple ID -- normally used for FaceTime, Messages and other services -- with your mobile phone number. It also sports a new user interface in line with iOS 6's general theme.
The App Stores have been redesigned from the ground up. Applications are stacked neatly, and the interface is far cleaner and easier to use.
The vast majority of applications for iOS 5 still work for iOS 6 -- even the quirky ones. Everything is a lot easier to see in the redesigned App Store. The same features are there -- from top charts to featured apps -- however.