Again, I can see arguement saying that Zelda is already an RPGish type game, so why rework it into just a different type of RPG. And I would agree if you were doing a story about Link solo then to make an traditional turn based RPG instead of an action adventure RPG would be silly.
But, I think there is potentially a really great story inbetween Ocarnia of Time and Wind Waker, that doesn't involve Link.
Remember, there was a great war and no hero of time showed up. Well what happened? which heros tried to rise to the task to defend Hyrule? This is an important story that could connect the stories and be really cool.
Personally, I would handle the story that the Sages from OoT came back to fight for Hyrule's future. This would give you a great diverse party system, that all have connections to Link, and reasons to try to save the world. It would be a game that could greatly expand the lore and mythos of Hyrule and Link. Square would be perfect for a game like this...and I think we would be pretty stupid not to be excited about something like that.