I think you should make a deeper story.
Some things that help are:
Give the character a reason to collect badges,
Give the player a reason to fight the evil gang,
Give the player a reason to do everything!
Here is an example from my game(the game is more centered around the evil gang.)
No, there won't be guns.
The player goes after the evil team because they kidnapped his father and even after saving him you still want revenge.
Try to make your story more interesting and deeper without straying too far from the pokemon formula.
There is a certain compromise involved.