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".
Well, no offence, but I personally think that none of the three proposals would fit in the Zelda Universe. Irrelevant to that, though, I think that it's generally kind of oblivious to decimate the central character like that at the end of a game when all the psychological attachments between the player and that character (which are the most important) have beed developed and solidified. Perhaps a Butterfly Effect or or a Tarantino videogame would be more appropriate for that kind of stuff, although I still think that watching a movie for 2 hours is completely different than controlling a character for 25 (also what would happen gameplay wise?). Tastes differ though so there could be some audience there for you.
As for the topic (deriving ideas for stories from existing games) I believe there's no better way for someone to learn or improve himself as a writer, than by analyzing stories of famous and successful videogames and trying to improve on them. This is just a place where one could come and get inspired in ways to make his stories better.