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It has been that way on the Nano since the 1G Nano, they probably decided to standardise it now and chose the bottom
 
With the original shuffle, I get it (with the lanyard accessory and so on). I've never really understood it beyond that. But I live fine with my Nano (2G) being this way.... you have to make some small adjustments, like if you put it in your pocket, you should put it in upside down (so that the jack doesn't mash against the pocket bottom).

But yeah.... I'd guess there's some other reason behind it, engineering-wise. The jack was a fairly common failure point on older iPods, wasn't it (my 3G fullsize is fine, but I seem to remember there were lots of people who had the jack go bad). Maybe that has something to do with it.
 
its at the bottom because then the headphone cable loops up underneath the ipod and doesnt fall down in front of the screen when the jack was on the top

i think
 
i think it is because when iPod's are in your pocket you put it in upside down and the controls make sense when you feel them( the right way up). On the touch i would say it is an engineering reason.
 
^Sounds like a good enough reason to me, as for the touch I hope either Apple or a 3rd party company comes up with some physical buttons that plugs into the dock connector for pocket browsing.
 
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