I feel that something like what's in the Ruby hack Pokemon Light Platinum, having a World Championship. For example, you beat the Johto league, then go onto to Kanto, become the champion of one of them. Then BAM! World Championship, all champions go up against eachother. Or maybe (And I'm just saying this because I love the idea.) we could go through every region, like start out in Kanto, beat it. Save and place pokemon in PC, move to Johto, begin with starter, beat it, put in PC... Repeat. After beating a new league, special events happen in other regions, like Kanto has a new upcoming opponent, DEFEND YOUR TITLE!
Sorry, if that all sounds crazy. The thing I forgot to mention, you cannot use your old pokemon until after you beat the new league.