Wow, can't believe this topic actually got this much publicity. Anyways, since I started this topic, might as well deposit my two cents.
I'd re-do Hoenn, completely. I'd remove all the 3rd Generation Pokemon (san certain ones like Torchic's family, Milotic, Kyogre, Jirachi, Deoxys, and others) and would rip that Arceus-forsaken region to shreads and rebuild it in a tasteful fashion. I'd leave the difficuly alone, don't see any reason to change it since it was just as easy as any other Pokemon game I've ever played. Now, the evil teams, oh the evil teams, I'd erase them and replace them with either a sinister team bent on capturing Jirachi and using its wish-granting qualities to bring the world to its knees, and make Kyogre and Groundon dormant legends that you find later. The plot was...mediocre at best, and like I said, I'd erase it and redo it completely.
Ya know...This actually sounds like a good idea...[opens Windows 2007 and begins typing the storyline]...hahahah