Nintendo has clarified the use of the Wii U GameCube controller adapter that will be released with Super Smash Bros for the Wii U. Apparently those who were wanting to use it with other titles will be disappointed to learn that at least for now it will only be compatible with Super Smash Bros Wii U and nothing else.
Part of the confusion comes from some wording that Nintendo suggested that the controller and adapter would be compatible with all Wii U games that made use of the Wii Classic Controller or the Classic Pro Controller, and the Wii U Pro Controller, but apparently this isn’t the case.
While Nintendo is apologizing for any confusion, the root of the confusion came from their own web site. We would not put it past Nintendo to release other titles in the future that allow for the use of the controller and adapter, but right now it will only be compatible for Super Smash Bros Wii U and that’s it.