I'm no expert, but I think the way to do this would be to start over and create a new mega zone, or perhaps break it into 3-4 zones that are just a rough amalgamation of all the old zones. But, if you're going to do that, you might as well just make a new world with a new story arcs and such so we just get more content instead of reproducing the old content. Oh, I know, lets make it an entire alternate Universe ...and it could have alternate versions of the current Heroes! And it could be ruled by an Emperor named, just of the top of my head, Emperor Cole!
Yeah... that sounds like it might work.