Actually, this is nothing new. Almost all devices powered by lithium-ion batteries exhibit this behavior, and it's only noticeable in the new iPad because of the huge battery pack it contains.
Here's the deal. The charging circuits inside modern consumer electronics are highly complex. They need to be, because the last thing you want to happen is to overcharge a big lithium-ion battery pack and have it swell up inside a device -- or worse still, overheat or possibly catch fire.
Charging circuits employ a number of tricks to help keep the battery safe and healthy. The first trick is to slow the rate of charging as the battery reaches its full capacity so as to avoid the risk of overcharging. You can actually see this in action when you change something up. You can notice how charging from 95 percent to 100 percent takes a lot longer than charging from 50 percent to 55 percent. This is deliberate and its purpose is to protect your battery - and you - from damage.
Another trick is set the 100 percent charge mark at a lower capacity, say around 97 percent and then have the charging circuit silently charge this remaining 3 percent while the device is still plugged to the charger. It's possible to see this in action too. Charge up you phone, but disconnect it as soon as it hits 100 percent charge and notice how fast it drops to 99 percent. Now charge it overnight and see how long it takes to drop to 99 percent when off charge. You'll notice that it takes a lot longer. It's a lot like filling your gas tank to the brim, it takes longer for the needle to fall from the full mark than it does is you don't fill it all the way to the brim.
Why are people seeing this with the new iPad but didn't notice the effect on other devices? Simple. The battery on the new iPad is huge, with a total charge capacity of a massive 42Wh or measured another way a monstrous 11,666 mAh. A 3 percent safety margin for the iPad 2 battery would be equal to around 210 mAh, while the same safety margin for the new iPad would be equal to 350 mAh.
My guess is that Apple will be able to tighten up the charging mechanism on the new iPad through a software update, but as long as you leave your new iPad plugged in for a bit longer, you should get the battery up to full capacity.