New data here. My new iPad 32 GB WiFi has been getting hot enough to go into shutdown mode when using the NetFlix App after 30 minutes. It gets very warm when viewing web pages with Safari but doesn't shut down. I am not using any case at all because I didn't want it to damage itself.
Here's the kicker. My brother bought an identical iPad at the same time I bought mine. He brought his new iPad over for comparison. Using the NetFlix App to watch the same movie on his unit revealed that his iPad only gets slightly warm. If my iPad ran at the temperature his does I would have no complaint at all.
This seems to indicate a quality control issue more than a design flaw. I think people having overheating issues should swap them at the Apple Store for a new unit. The new iPad is capable of running relatively cool but some defective units have gotten into the supply chain.
I don't have any 3D games to really stress my iPad with but the Netflix App is enough to cause my unit to shut down fairly quickly. This simple comparison between identical units as described above shows that if you have a defective iPad, it will run too hot no matter what Apps you use it with.
Apple should make a press release soon to get this situation under control. The "iWaffle Iron" jokes are already spreading in forums and email.