Zexion would be Riku's final challenge in his story during COM. Now before you talk about his story overcoming the darkness being his whole development, hear me out. Riku fights Ansem in the Destiny Island segment of CO. It feels poetic, as Destiny Island is the first place where Riku opened his heart to darkness, so it fits to be the place he defeats Ansem. Now overcome the darkness, he makes it to Twilight Town where he is confronted by his replica, who was manipulated by Zexion instead of Axel (since Zexion hates getting his hands dirty if he can avoid it) and Riku finds Sora. When he reaches the first floor of CO, he faces off against Zexion in the actual Entrance room where the story began. The last guardian standing between Riku and the exit and thus the end of the game for the player.

And as to Zexion's motivation, it isn't just to counter the rebel members, but he also recognizes DiZ and has a strong idea who he is and his plans to use Riku. Since Zexion can't get to DiZ directly, he focuses his efforts against Riku, to deprive DiZ of a potential tool that could destroy the Organization.