That whole ending sequence was so ginormously meta, I'd bet one of my spare kidneys that Yahtzee got the idea after playing "The Stanley Parable" one too many times. It'd probably be fine as a twist for, say, a fan-game of the Zelda franchise, but would probably start a riot if actually produced by Nintendo as part of the main series.
That said, I would like the story to be shaken up just a bit compared to "Ganon kidnaps Zelda, Link has to save her" bit, and would definitely think that characterizing the main trio beyond "good guy, good girl, bad guy" is a step in the right direction. I even have a little story idea of my own, which will most certainly twist around characterizations, by way of adding a new force.
Basically, the premise is supposing another villain (hereinafter to be codenamed "Mr. X") kills Ganon before he even starts building his empire of evil to hunt down Zelda and Link, and uses Ganon's Triforce of Power to build an empire of his own. Mr. X's empire grows more quickly and ruthlessly than Ganon's empire could have ever hoped to because Mr. X uses the Triforce of Power to power an energy generator, which, in turn, allowed him to transform the kingdom into essentially a gigantic industrial sprawl. The visual cues of this empire would mostly be of a "fantasy industrial revolution", like Albion in Fable 3 or Dunwall in Dishonored, with rifle-carrying soldiers replacing standard medieval-era mooks.
This huge societal upheaval by Mr. X is carried out when Zelda and Link are barely children in this timeline (or even yet to be born), so they end up brought into severely different lifestyles - Princess Zelda is raised as the socialite daughter of one of the bickering bourgeois families of the upper class, while Link is slaving away in one of the factories or mines below. In this case, Mr. X's transformation of the civilized world had also rubbed out the whole "Legend of the Triforce" thing from the mass consciousness, and the only people who know about it are Mr. X's inner circle of cronies and henchmen, and a few elderly survivors of the era before Mr. X's rise to power, with neither Link nor Zelda knowing of their legacy.
The game starts when the forces of Mr. X are able to realize that Link and Zelda are carrying their respective Triforces, and Link (and possibly Zelda, for a potential secondary campaign/co-op spin) is barely able to escape, joining a scattered group of rebels in the outskirts of Mr. X's kingdom. For the record, the whole "chosen ones" business isn't recognized as such, with the rebels only wanting Link and Zelda by means of Mr. X wanting his hands on the two himself. Link and Zelda themselves would have rather preferred to leave the whole mess behind them, but the forces of Mr. X prevent them from doing so, only for character development overtime to give them both an acceptance for their given destinies, as well as maturing enough as fighters and leaders to lead the people of Mr. X's empire (at first even MORE skeptical of the whole "chosen ones" business than Link, Zelda, and the rebels) into a full-on revolution.
The climax, where Link and Zelda storm the building Mr. X was using to harness the Triforce of Power, has them stumble across the big reveal of the story - that, while Ganon was "killed" for Mr. X to gain his piece of the Triforce, his spirit still lives within the machine powered by the Triforce, and has since gone completely insane from his torturous imprisonment. Even if he ends up being the final antagonist, this would definitely earn more sympathy towards Ganon based on the hell he went through, as well as him realizing how futile it is being forced to evil by being the reincarnation of the demonic prick responsible for the whole mess (slight Skyward Sword spoilers there).
Technically, it isn't a complete deconstruction of the Zelda games, but definitely more than enough to shake up the box, and hopefully put down lots of different gameplay innovations to go with the new story.
