Wii MotionPlus, which is the only Motion Controller that Skyward Sword works with, was released in 2009, the Zelda team had just finished Phantom Hourglass in 2007, so work started in 2008 at the earliest, and then they were also working on Spirit Tracks.
So 2008 Skyward Sword was conceptualized, 2011 is when it came so.
So yeah, it still ended up taking 3 years to develop.
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