Actually my MacBook Pro (2011 17" quad-core) does the same thing. During very heavy load it will not charge and actually drain the battery slowly. I've read on the MBP forums that this is normal, though obviously not ideal.
Always trade-offs. Apple could have included an even bigger battery or charger, but then even more weight. This is probably not a big deal for most iPad users.
I have the same issues with my MacBook and not charging during heavy load use.
The only noticeable difference for me on the iPad 3 is the weight, and I wouldn't want a bigger battery, nor a fan in this.