Have no fear! Nintendo released a video detailing how to transfer your data from the old 3DS to the new one. The process is pretty much painless, but it might take a lot of time depending if you have a lot of items to transfer over.
Those who bought the Majora’s Mask or Monster Hunter 4 Ultimate bundle, it’s possible to transfer the pre-installed game. Just make sure that you do not link the new Nintendo 3DS that you just got to any Nintendo Network ID.
Anyway, here’s the video: