I don't think theywould bring it that far into the future. I'm hoping that it will take place, when technology is beginning to emerge in Hyrule, and shifts power between the gods, to those who posses such technology.
Maybe the main villian would be a leader of Hyrulians who want to move into Technology, and rule the world with there newfound powers. He actually has hyrulians as his army!
However at the end of the game, after much anguish, When Link finnaly is face to face with him, and his trechnology is almost all diabled, link realizes the one final step that this man will go to, he will fuse his technology, with magic, and take a finnal desperate stand against link, in the most epic battle ever contained in a zelda game!!!
I think it would also be pretty coolo, if at the very end, a cutscene emmerges, where this evil leader tries to resurect an acient evil(Ganon), but in turn gets destroyed by the great power it takes. And link gets a finnal look at Ganon before he returns to where evr the hell he is!
