When Apple released the new iPad, the price of the iPad 2 got cut to $399 (16GB). The price is apparently not all that changed. Apple also updated the A5 CPU to the 32nm technology. According to AnandTech, the iPad 2,4 is getting 2 hours more battery life because of that compared to the iPad 2,1.
The problem is that it is almost impossible to tell yet if you get a new iPad 2,4 when you go an buy a $399 iPad 2. The boxes look identical. The only way to tell is switching it on and check the iOS version number. The iPad 2,4 comes with iOS 5.1 pre-installed and the old stock comes with iOS 5.01.
Anandtech says that the iPad 2,4 is still very rare. You might just wait a bit until the new wave of updated iPad 2 is washing into the retailer shelves.