I've always thought Ienzo and Aeleus were more important than CoM led them on to be. Zexion had the brains, and he had the time; it's possible he knows a lot of things about Castle Oblivion that Axel never found out. So his role could be helping the heroes to find Ventus (assuming they don't just get Aqua to do that), or more likely, as a strategist, to help plan the battle against MX.
Aeleus, as Lexaeus, seemed to be very protective of Zexion and a true friend. We never saw much more than that, but at least that much was apparent. And while he may not be on the intellectual level of Ienzo or Even, he was probably one of the smartest members of Ansem's apprentices, as his Nobody was placed in the basement levels to help conduct research with the aforementioned apprentice's Nobodies. So while his role probably won't be as grand, I see him continuing to aid Ienzo, perhaps even developing something that will aid in the defeat of MX.
