Now that the new iPad has been put through its paces, there have been reports that iOS 5.1 is not accurately reporting battery charge percentage. ZDNet has even said the battery algorithm is "busted" while other reports have warned against overcharging the device. For those who are worried about damaging their batteries, rest assured that the iPad is not destroying its own battery.
First of all, every iOS device will report a 100% charge while leaving room to spare. This keeps the lithium-ion batteries optimized. The iPad 3 battery is massive, clocking 42.5-watt-hours compared to the iPad 2's battery at just 25-watt-hours. As a result, iOS may be reporting the new iPad battery as fully charged when in fact it's only at 90% capacity.