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Incorporate more RPG elements into the games. Somewhere near the beginning of the game, you choose a Trainer Class, much like the many NPCs you battle in the game. In addition to exclusive clothing options, your choice in trainer class encourages you to specialize in a particular Pokemon type. For example, if you chose a Blackbelt trainer class, fighting type pokemon in your party would gain more EXP in battles, be easier to catch, or even have slightly higher stats. You would not be allowed to change class until after you beat the game, if at all.
In addition to this, after you beat the Champion, you are given a gym all of your own to lead, and to customize. You are able to recruit various NPCs of similar trainer classes that you have battled before to be a part of your gym. You can change the layout and make puzzles as well. You will then be able to share these custom gyms with people online who will be able to battle them all they like. Think of it kinda like Dampe's Shack in Links Awakening
