I think that an offshoot game like Tingle's Ruppeeland with Zelda as the main character is a great idea, but making a game like that as part of the main timeline would take away from what the Legend of Zelda was originally about--A hero rescuing the princess and saving Hyrule. I can't imagine Zelda fighting an Iron Knuckle or a Moblin.
As long as it's not just "Zelda decides to go fight baddies herself!" with her abandoning her duties as the princess. I'd hate to see a message of her being a good character because she's fighting, I'd rather see her in a way that makes sense for the ruler of a country to be.
Potentially something when the Hero of Time didn't show up, Ganon is winning, Zelda has to flee Hyrule Castle Town. It's before the flood, Zelda's fighting to try to reclaim the kingdom (makes sense for a leader to be on the front lines in that way). It'd be a bit of a downer ending, but it would be a fantastic story too. Maybe even have it be like... yeah, Hyrule floods, but Zelda is able to lead some people to an island they can live on until the waters reside? Not sure.
I contest anyone who claims that Zelda couldn't go on an adventure of the same caliber as Link.The ones we have seen so far? Of course, it's hard to imagine Twilight Princess Zelda solving dungeons, but then, it doesn't have to be Twilight Princess Zelda. Or any other Zelda we have seen.
Really, don't forget that with this series changing a character is incredibly easy. A game starring Zelda doesn't have to be like Super Princess Peach.