Indie developers outside of Japan can still apply.
Indie developers based in Japan cannot apply to develop applications for the Wii U at this time.
Despite the growing industry support for indie developers across the board, a Nintendo form on the GDC (Game Developers Conference) 2013 website states, in English and Japanese, that Nintendo is currently not accepting applications from Japanese indie developers.
According to a statement given to CVG by Nintendo, “The policy in question is the decision of Nintendo's department responsible for licensing activities in each region, and the licensing department of Nintendo is currently not accepting subject applications from individuals in Japan.”
Since no further details have been issued regarding Nintendo’s future plans for Japan based indie developers, it is uncertain if and when this policy will change. Nintendo will, however, continue to accept applications from developers outside of Japan.