@super_mario_john said:
I doubt the Virtual Console stuff will ever be shut down, since it would make way more sense to transfer all of that functionality to the WiiU and whatever other consoles they make in the future. They might update it and change it, but I think the only way it can disappear entirely is if Nintendo goes belly up, which most likely won't happen.
I am pretty sure that is what will happen. They will have DS games for the eShop of the 3DS and you could transfer your games over. I guess they will have the same transfer between Wii and WiiU and keep all the existing games up, VC and Wiiware and then add WiiUware and probably Gamecube games to VC. I wouldn't be concerned about it. I think Nintendo will get this right.

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