Nah. Zelda is essentially a story about heroes, adventure, and exploration. There's really nothing to gain from an "evil" story.
I agree with Hanyou here, but I have something else to add.
While heroism is probably too heavy a subject in the Zelda series to include such a thing as playing like the villain, I think it's interesting to notice how it's gone
slightly towards that sometimes by blurring the lines.
Take for example how Ganondorf's motives in Wind Waker could actually be considered good depending on how you look at it and how the king of Hyrule admitted to be like him in a sense, despite being the wise one in that scenario.
Also, I feel that bringing up the now famous Lanayru cutscene from Twilight Princess would be interesting.
[video=youtube;cWlJ2Zk62rU]http://www.youtube.com/watch?v=cWlJ2Zk62rU[/video]
Maybe playing as the evil one would be going too far, but it's hard to ignore how far they've gone with blurring the lines sometimes.