This October, Nintendo will ship an updated 3DS in Japan called "New 3DS." This tweaked 3DS includes a tiny analog stick on the right, built-in NFC, two additional shoulder buttons, and an improved CPU.
The updated 3DS isn't expected to arrive over here until sometime next year, but the new CPU is already creating some wrinkles. For example, Nintendo announced a port of Xenoblade Chronicles to the 3DS, but it's only for this new 3DS, as it takes advantage of the CPU. It won't run on the 3DS you own right now.