Honestly this was just poorly planned. And not even Pokemon Bank - I bought Fire Emblem on the 11th and getting in to download DLC wasn't working well the two days after, maybe because of the new Network ID thing they debuted? That's been happening a lot even before Christmas. Then, you combine that with Christmas and people getting all kinds of new Wii U and 3DS systems, getting gift cards and eShop cards, trying to download games, trying to use online stuff AND Pokemon Bank debuting all around the same time in other countries...it was bound to happen.
It's interesting to me though that it seems the Bank is letting some hacked Pokemon through, you just can't use them in online battles. At least they're doing that much.