If a newer (not sure if it's the same with pre-intel macs) mac laptop gets too hot, it till put itself to sleep to protect itself. It sounds like your problem isn't so much that it won't wake up when asked, it's that the machine is overheating.
Take a look at your system log to see if this is the case. Look for something along the lines of "emergency overtemp warning, going to sleep".
First thing is, where are you charging the mac? on a table? on carpet? in a bag? Anywhere with poor air circulation is definately a bad thing.
-Try charging it with the screen open. That will allow a lot of heat to escape through the keyboard.
-Can you hear the fan spinning up when the machine is getting hot? if not, there could be a problem with it. (or possibly the temp sensors that should tell the fan to spin up).
-The battery may be on it's last legs. All batteries will heat up to some degree when they're being charged. If it's excessively hot, it might suggest a problem with it.
Try running the diagnostics on the install DVDs. They're not an omnipotent cure-all, but they might shed some light on it.