I was just thinking of something like this when I posted in the 3D Link to the Past thread, but I didn't put my idea in full...

What I was thinking was, what if a new incarnation of Link, sometime after Link to the Past and Link's Awakening, must be sent back in time to make sure that the events of a Link to the Past actually occur? Hence, the cameo appearance of the 3D LttP. It could involve having to trick Agahnim into being Ganon's puppet - grim, but what if the alternative was even worse?