Being in a case does not allow the battery to "breathe" the heat out of the aluminum back as efficiently. Next time maybe take it out of the case and see if it gets warm .
Mine, Ipad 1, gets slightly warm on the back with extended use but it only lasts a few seconds after usage. I keep mine naked while using most of the time, have a Zagg mate keyboard/cover combo I use when the unit is not in use.
Hope that helps
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