Well first of all, I don't think this could shed any light on the origins of Twilight Princess, since I feel there it too much of a time gap. However, I like the idea you're raising.
A continuation of one the most epic tales and within one of the most significant set of events, is catering to the average Zelda fan. That's one thing I think this could potentially bring, large attention and immediate positivity from the fan base. I know there could be the odd fan here and there, but I think we want continuity in some format and where better to look than the most significant hero across the history of Hyrule.
It could be very possible that the Hero of Time isn't necessarily done with his adventures. He returns to Hyrule, but he's still on a journey to find Navi. Since Link was going out of his way already, does this mean that he would venture to the outer reaches of Hyrule? Os problem with this would be that it could feel like another Majora's Mask situation, there isn't necessarily anything wrong with this bit it lessens the idea of continuity.
One possible plot point I could see is Ganondorf ready for execution, but an evil tires to save him in order to bring Hyrule into darkness once again. Thinking about it, we could have an older Link (think Assassins Creed Revelations. Link now a laid back mature figure is called upon to redraw the Master Sword and try and stop the rescuing of Ganondorf. Looking more deeply into this situation, I like it, I doubt we could ever see such a thing but I can definitely see how it could work.