I think that most game designers can think of at least 20 different what-if outcomes of already existing stories in about 1 hour. The clue is to try to come up with an entirely unique storyline from bottom up. I think your procedure could be a nice way to find those stories though, like first thinking about existing games and alternatives within that, and then create something unique based on it.
- What if Link and Ganon were actually the same person and Link realized this at the end of a Zelda game?
- What if the Ganon that Link fought was actually Zelda in disguise, as a puppet under the control of the real Ganon. So he makes you kill the one you're trying to save.
- What if Link is actually Zelda, and in reality it's Zelda trying to save Link from the King, and Ganon is her benevolent father? and Epona is a dragon smoking a pipe.
One of the great qualities of Quentin Tarantino, for instance, is his ability to take the viewers expectations and turn it completely upside down.
He's a master of the "WTF moment".