well, maybe in the second part, after you get the champion in jotho, a ship will bring you to tascan, a region with 6 more leader, to become the cchampion there, tehre are the 4th generation pokemon, and you should not use the old one, or the leader are stronger, too.
and a new organisation, which is found by an rocket grunt wich want to be the king of world alone, make you a hard live, again.
maybe this is a good story, as the pokemon which the new team watn to, you can take a always shiny latias or latios, becaus tey look like red and green yade, an they have maybe the power to make old iron to yade
i hope you understand me, my english is very bad :'(