Is it the Wii U or The Legend of Zelda in General in Japan? The Wind Waker HD mades the most horrible Debut of a Zelda Game ever in japanese sales. Since it's launch on September 26th, the Game sold only 30.000 Copies. You barely find it on the Amazon Japan Bestseller Charts. Even for a Wii U Game, this is pretty bad. Let's take a look at Pikmin 3, it sold in it's debut week over 60.000 Copies. The japanese Miiverse of Wind Waker HD is also pretty empty. About 11.000 Posts. The game is available in Europe since Yesterday, and there are already about 15.000 Posts.
Well, you can say the game did not sell well because it's a Remake and the bad sales of the Wii U, but look at Skyward Sword, it was also a commercial Failure in Japan. It sold only about 360.000 Copies in Japan. In the US and in Europe, the Game sold over a million each. Let's go back to the past even more. Twilight Princess, a Bestseller in the US and Europe (sold over 3 Million Copies in the US), sold only about 600.000 Copies in Japan.
This reminds me of Kingdom Hearts, some sort. Kingdom Hearts is also a Franchise, not selling millions in Japan. It's not even popular among these people. I, for myself, was not aware The Legend of Zelda is not that popular in it's Homeland. What could be the reason behind this?
Anyway. Besides of "Zelda is not that popular in Japan", I can't believe Nintendo will be impressed about the 30.000 sold Copies of Wind Waker HD in Japan. But, from what I've heard, Japan did not even got a Limited Edition.