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animegaming said:
cause outside of Majora's Mask every home console Zelda game was built from scratch 

Twilight Princess used the Windwaker engine as well. But still a lot was changed barely making that matter. 

http://zeldawiki.org/The_Legend_of_Zelda:_The_Wind_Waker

Contrary to popular belief, programming the game with an engine based on this style was more difficult than programming Twilight Princess, after modifying said engine, to favor realistic graphics