New iPad Runs About 10 Degrees (F) Hotter than iPad 2 [Updated]
Both in our forums and Apple's Discussions, there have been observations and complaints that the new iPad runs warmer than the previous generation. The phenomenon was noticed in TechCrunch's review of the new iPad where they said:
One other slight downside which I have to assume is related to either the battery or the LTE functionality is that unlike previous iPad models, the new iPad does get noticeably warm in the lower left corner after prolonged use. It’s never hot, just warm. But again, I never noticed this on other models.
To investigate further, Tweakers.net (via Engadget) took thermal images with an infrared camera of both the iPad 2 and new iPad. After running GLBenchmark for 5 minutes, the hottest point was measured.

The hottest point on the new iPad was the lower right corner which measured a temperature of 33.6° C (or 92.5° F). The iPad 2, meanwhile, topped out at 28.3° C (or 82.9° F). The difference between the two was 5° C (or ~10° F).
There seems to be a mix of responses from end users, with some not noticing any extra warmth at all, while others claim it gets uncomfortably hot to handle. It seems that the use of heavy GPU apps such as games may be a factor. The added heat seems not to affect the functionality of the new iPad.
Update: Apple released a statement to The Loop about the heat complaints.
“The new iPad delivers a stunning Retina display, A5X chip, support for 4G LTE plus 10 hours of battery life, all while operating well within our thermal specifications,” Apple representative Trudy Muller, told The Loop. “If customers have any concerns they should contact AppleCare.”
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