The biggest problem with backups is the effect they have on online cheating. I think Nintendo does a good job cracking down on hackers though.
Ahh..good point. Online should prove to be a decent measure against it. I do agree that the amount of people willing to go through this will be minor but when it's moving this fast, I can't help but be concerned. This could indeed become another DS or 3DS situation especially since this isn't Nintendo's own hardware. And the Pokemon games have been downloaded tens of millions of times each online.
But maybe I'm overacting, and something else I forgot to mention is that to currently do this method you need a $30 device from Team Xecuter to even get backups running so yeah this is definitely limiting the potential customers.