I think if your looking for a well developed story rather then a contrived one then the Zelda series is probably not the series for you. Not that I wouldn't think a epic well thought out story wouldn't be a welcome development, but Nintendo isn't really that innovative when it comes to the story. For them it is a very distant afterthought.
The truth is you want Ganon in the next game, because it gives you a glimmer of hope that the series can finally break the cycle. Once Ganon is dead it will free the series to have a ongoing story rather then a recurring one. In fact in a dream scenario the next game should start with a new Link finally killing him for good, and then the Triforce of power can be dispersed to a new cadre of villains. With more characters the story can see a very needed widening. That way you can have more good guys, and more bad guys. Hell might even let Nintendo sandbox out the world.











