It doesn't matter if it runs hotter than the iPad 2, that doesn't mean it's running TOO hot. The back casing gets to 33.6degC according to that article, that's not very hot at all, all things considered. The fact the back case is made out of aluminium means the heat of the internals is being effectively conducted away from the internals which is a good thing.
Just because the new iPad runs hotter than the iPad 2 does not mean it's bad. As long as it's within specification and isn't negatively affecting the internals than it really doesn't matter.
I am quite sure that Apple has done very extensive testing on the device (as I am sure they are legally required to do, especially given the large battery) and found it to be fine.
Relax people.