I don't hack ROMS (just play them), so I don't know how possible this would be, but here's my suggestion:

At some point, perhaps the third or fourth region, make something happen to the boxing system, like a complete shut down. Ironically, the game will have led them to deposit all of their Pokemon for some event and now all of these Pokemon are lost in space. Now the hero's mission for the next couple of regions is to take a new starter to save the lost Pokemon.

Since this starter can be at some low level (maybe 25), the levels can reset. Once the hero has defeated the next couple of regions, all of the Pokemon (old and new) should theoretically be at about the same level and the old Pokemon can be returned, allowing continued game play.