I like the idea of a Zelda RPG that doesn't necessarily include Link and extends the canon. It's just the kick in the pants the whole franchise to find something new and fresh, and RPGs would be new territory (as far as I'm aware) for Nintendo. I may be warm to the idea in part because I had similar thoughts awhile back about a possible Zelda RPG that would take place during the Hylian/Sheikah alliance a few years ago. Plotwise, it was very different from yours so I may make a thread about it, though I don't want to be accused of ripping you off. Regardless, not all stories about Hyrule need be Zelda games--some can be just as effective, just as resonant, if they take a different path. The flood, being as pivotal as it is, would be a great place to start.
I do have at least one gripe. I disagree with you about Ritos evolving from the Zoras, and I just wanted to take note of that--though that's for another thread. Another thing I'd be careful of is that I worry this ties too closely with The Wind Waker. What I mean is, if this were a real game, I'd be critical of how much it tries to reconcile OoT and TWW, in a style almost reminiscent of the Star Wars prequels. That's not to say it's mediocre, but that this game as imagined would need to stand on its own so that it could offer more to the universe without overcompensating. Given the synopsis, it seems to overcompensate just a bit for my taste. Of course, it's just a synopsis of a game that doesn't exist, so I could very well be misjudging.
I do like the twist on RPG cliches--what makes a good JRPG story in my book is that it can successfully manage those cliches, turn them into something new. Take Skies of Arcadia. You had your meek, mysterious character, your pirates, your power character...I don't want to spoil the game for those who haven't played it, but it's chock-full of well-managed cliches. Your synopsis doesn't avoid these things. What it does is put a unique "Zelda" twist on them.
One last thing. Some fans overplay the "dark" aspects of the franchise, forgetting that it's also got a lot of quirky humor. This doesn't seem to fall into the "graaaaaahhhh! GIVE US AN M-RATED ZELDA!" category. The inclusion of a deku scrub and a Kokori is ingenious, and would probably help keep the game light. From what I've read, your hypothetical game wouldn't take the series down the boring, adolescent, angsty path of darkness and endless "mature" content, even though your plot deals with fate and apocalypse. For that, you should be commended!