Thanks for the Comments
I've just had an idea for the Game-Play. My original idea was Link goes around the present entering 'Time-tears', which are pockets of 'No-Time' the Monsters are using to enter, and which were greated by the Destruction of the Temple Of Time, closing them and slowly restoring Time to it's natural way of things.
However, my NEW idea is instead of allowing Time-Tears to appear, the destruction of the Temple Of Time has destroyed time itself, and when you escape from the Black Citadel, you are sent between time-lines as you try to fix time.
So the whole game is you diving from one time-line to the next, trying to get back to your own time-Line. Of course in the process you encounter Gandon and manage to save Hyrule and the World, but hey, when has link NOT saved Hyrule and the World???