According to customer service rep David Marshall over at Nintendo, the 3DS and Wii U will use a combined account system between the two akin to the PS3 and Vita’s interactivity. The new account system will arrive with Wii U’s holiday season release in the US and Canada, then transition over to 3DS.
Nintendo has already offered some safeguard details up. If you have an issue, you can take either unit to “Authorized Service Centers” and maintain the combined accounts. Even if your completely lose one of the devices, these authorized dealers can transfer your info to a new system. This setup, along with the fact that Wii U’s online will be free seems to tie into the potential self-sustained network Nintendo is shooting for. We’ll see how things begin this holiday season when the Wii U arrives.