According to Nintendo, a new update for the 3DS this December that will allow users to use a Nintendo Network ID and Miiverse on 3DS along with Wii U. Whether the ID will replace Friend Codes is confirmed or not.
EDIT: Users will be able to create a new ID for their 3DS, or if they have a Wii U, they can link their 3DS with their Wii U ID, which will also link the two system's e-shop funds.