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They tweaked the box when iOS 7 was released because it was a massive redesign therefore they sort of had to change the packaging. However I doubt they do this every time for old devices, it was just that year with iOS 7.

Whenever there was a major change to the OS that added icons, changed the way they looked or changed the layout of them Apple changed the box. Take the original iPhone for example, even though that phone was only sold for a year it had two different boxes; one with the original OS pictured and one with a later version of iPhone OS with the iTunes Music Store.

iPhone 3GS did the same thing. It was sold after iOS 4 and 5 so the box was changed each time. Same with the 4s; in fact I have a 4s that was bought after iOS 6 launched with the 4s shown running iOS 6 on the box. Quite interesting how serious Apple takes these things. I think the iPhone 6/6 Plus and iPad Air 2/Mini 3 boxes are designed not to show any iOS running so they don't have to constantly be changing the picture on the box. The iPad boxes are in profile so it doesn't show the screen and the iPhone boxes are just embossed with the outline of the phone.
 
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