As The OB says, the iPad 3 has a large battery and a high res screen and has powerful graphics. Also, it is passively cooled....all that means heat builds up. Thus, you need to either ramp things down by lowering the screen brightness, limiting your play time, or providing some cooling. A good idea is to use headphones for sound and then play under a fan...with the fan blowing on your iPad. It works best if the iPad is not in a case, in terms of cooling, but that may be more uncomfortable for you. You will need to experiement to find the best combination of cooling techniques for you. Turning on the AC helps, too.
I spend a lot of money to keep the cpu/gpu in my computer case cool...so I can encode video, play games, etc, while keeping things cool. The iPad is no different, but it does tend to push a lot of pixels while inside a tiny case (comparitively). My Nexus 10 does the same thing, but it will throttle down the GPU (lower the clock speed) and then it will start dropping frames, which means game play becomes laggy. Again, cooling is the key to controling this. Same techniques apply.