While the larger battery may be contributing slightly to the temperature increase it is more likely caused by the electronics in the iPad not the battery. Yes the battery is larger because it needs to deliver more power for the new CPU/GPU, memory and display but batteries are designed to deliver a steady power load over a given time period for a specific resistance. The heat is generated by current flowing through the "load" or in this case the electronics.
Since most of the reports indicate the heat in a very localized area this would point to a component or group of components on the mobo of the iPad. Plus if you think about it, the batter is spread out inside the case. If the battery were the cause of the heat it would be across the area that is covered by the battery and not localized to a specific area as described by many people. Although you will get some heat transfer due to air movement within the case and the heat transfer properties of the aluminum back side of the case.
Also when you consider the new hardware it's easy to see why you need more power and therefore why you are generating heat. First you have 4 GPU cores, that's 4 x the power of a single core GPU. Second, there is 2X the memory which is going to draw 2 x power and you have a display that has 4 x the pixels so you know there is a power draw there.
The real question, which hasn't been answered is whether the heating will be a problem once we get into the warmer months of summer. Heat is not good for electronics, hence the warning message you get if you leave your iPhone in the car on a hot summer day.