A number of things
1. There hasn't been a Zelda game to reach 1 million copies sold in Japan since Ocarina of Time
2. Zelda games are far more popular in the West than in the East.
3. around 10-25% copies sold isn't all that impressive when each mainline series title usually sells around 3 million copies. For example just 370,000 of Skyward Sword's 4 million are from Japan, which is even less than 10%. I mean, Kirby sells more than Zelda over there. A spinoff of Animal Crosing (Happy Home Desinger) has sold around the same or more copies than A Link Between Wrolds, a mainline 2D Zelda game, with around 32 million if its sales in Japan.
Zelda is just not all that popular over there.
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