With the holiday season coming around, Nintendo's servers have been experiencing some huge issues from the sheer volume of traffic. From what I've heard it's half the large amount of firmware updates (both for Wii U and 3DS) being downloaded, and half from a new feature in Pokemon X and Y that was also being downloaded en masse, despite only being available in Japan at the time. The latter has been taken off the market temporarily to help mitigate the overload of traffic, so it's only a matter of time before the servers will be working properly again.
In short, this issue will likely blow over in a few days. Hopefully. You can check here every once in awhile to see if things are any better.