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I've never been impressed by most of those "Be the champion or a gym leader!!!" ideas, almost all of them sound cool on paper and they always end up really shallow and probably wouldn't add more than an hour of game time max.
That said, they could repurpose existing mechanics into something similar. Just have the player "retire" from being the formal Champion after he wins and give him access to a small town with an old unoccupied Gym that you take over. The Gym essentially acts as a more functional Secret Base - you can pick a theme, decorate it with items, populate it with NPCs given different roles similar to the Join Avenue secretaries, etc - and the town is an improved Join Avenue altogether, where you place stores and shit in predetermined plots.
There, Champion continuity, Gym Leader wannabes, Secret Base fans and town building all rolled into one.
