How about this: instead of using traditional roles like Knights and Mages who only use physical attacks or magic respectively, use the roles provided in XIII - fighters who can use both but either excel at heavy damaging or weakening enemies. It's a different approach on classes, but it's classes nonetheless.
In essence, assign two or three roles to every party member and level up ONLY THOSE ROLES. Say you make Lightning into a Commando + Saboteur. In that case, never ever touch her Ravager, Sentinel, Synergist or Medic Crystariums and instead only ever invest CP into her Commando and Saboteur Crystariums.
That would keep the characters distinct from one another and give them each their own strengths and weaknesses. Now it's only a matter of actually managing to beat them game that way...