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Couple different ways possible I can think of:
1) Revamp level system so each level matters more, and you're ending kanto at 20, johto at 30, Hoenn at 50, etc
2) Find a way to make the player leave their pokemon from the first region in that region and start over like Ash, then pick the best of the best for the final elite four run. Maybe let you use any pokemon you have in a region once you clear it
3) Find a way to realistically delevel you pokemon. I.E. Your team of Charizard, Mewtwo, Snorlax persists into johto, but they are level 5 now, but still fully evolved. Probably not a good choice, now that I've typed it up.
I think I like option 2 the best.
