Being one of the people who got banned, I'd just like to say a few words.
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I realize what happened is my own fault, and I have no one to blame but me. Not Nintendo, not GameFreak, nobody.
I knew that the moment I modified my console, stuff like this could happen and I took the risk. Also, I knew that playing an unreleased game has risks.
The reason why I took the plunge on the 3DS and not, say, my Vita or PS3/4, is because when it comes down to it, Nintendo's online services aren't as important to me as other services like PSN or Steam or XBL. I mostly play SP or local multiplayer. But I realize that isn't the case for a lot of people.
That said, it is a shame that this happened, especially since I have spend several hundreds of dollars on Nintendo games, and several 3DS units and other consoles.
Here's to hoping that it's a temporary ban, and this can be cleared up with the passage of time. I wish the best of luck to all affected by this.