I like the core concept here. Based on the game story, I envision each number next to a character drawing that matches the enemy. As you click the weaker one, they transform into the copy of yourself. That will help unify the zones, too, once they change to your color as you progress. Since this is set up as a sort of puzzle, what could help make this more challenging is making multiple answers a right answer, so the player has to look ahead to plan more. If you didn't want to make it number based, you could come up with a sort of rock-paper-scissor system of winning, but use elements (e.g. fire beats earth and air) or something like that.
There are definitely lots of possibilities depending on the direction you want to go. Then you can add some really nice audio and flesh the rest out. Good luck!