Interesting. Looks like all the confirmed banned users have been using 3DS roms with public headers. The one rom I use online mainly is a personal dump of my Alpha Sapphire game. I no longer own the game though as I had to sell it to Gamestop to pay for fixing my other 3DS that got bricked.
I'm assuming CIA files will be safer to use online. I've already converted my Pokemon games to CIA installs as I discovered that using SaveDataFiler on them wasn't a big of a pain as I thought it would be. (turns out, you just need to use R+X to delete the "Secure Value" prior to importing a modified save. That way you don't get that "Save is not compatible" error when the game boots up.
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CIAs don't use headers, so it will be more difficult for Nintendo to detect them and the bans that have been going on seem to be aimed towards Sky3DS users using public headers. (I would assume this could impact Gateway users too, but most of them would be using CIAs anyway)
Just a day ago I took a modified Omega Ruby rom online for a hackmon FFA session. (my personal header for Alpha Sapphire is compatible with it) and did not have any issues. Of coarse I'm not stupid enough to try and take my hackmons onto rated battles on Battle Spot. That's straight up cheating and I don't do that.
For those curious as to how my hackmons work online, the trick is creating new mega evolutions. There's certain things about how the game handles online games that allows the "host" to define the stats of pokemon as well as mega evolutions. I've only done this in FFAs with other people that have been made aware of it and agreed to it. I won't go into too much detail as I don't want any one with ill intent to attempt this.
Long story short that hasn't caused issues for me either. I'm guessing bans will occur for public headers for 3DS roms that are mass distributed via torrents/rom sites and those will be easy for Nintendo to spot.
I'm pretty sure CIA/Private Header users will be safe from this. Even those using "modified" roms online. Given that they are careful with what they use them for.
I can already see the great decline of Sky3DS users starting. More and more of them will start getting banned from online games and the only solution for them is to buy a whole new console and perhaps even have to make a new NNID. Sky3DS can't simply make a new card with a different colored button to get around this.
Then the next major firmware update will likely block it. Sky3DS users have the false belief that just because Sky3DS survived the last few updates, that it will survive the next one are living in blissful ignorance and will be in for a shock.
I still believe 10.0 firmware or one soon after that will block Sky3DS entirely. Mark my words! I don't see very many buying yet another $100 Sky3DS with a new colored button to get around the block. This on top of the online bans will really hurt Sky3DS.
