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The main physical difference between these two devices are their specifications, the Apple TV 3 has much higher specs. For the time being this translates only into the ability to output 1080p to the TV. Whether or not it will become capable of other things that the Apple TV 2 cannot do, we do not know.
The Apple TV 2 and the Apple TV 3 can both run the same software. The only difference between the two boxes is that the Apple TV 3 box has 1080p stamped on it.
No, I do not believe that the Apple stores still sell the Apple TV 2, there will be little point to that, it was the same price as the Apple TV 3 and who would want that when there is a higher spec version available. You may however find refurbished versions available at the Apple Store.