I think it'd be really cool if in one of the arcs our primary antagonist deployed an attack on Wizard City (right out of the playbook of Malistaire) as a distraction, forcing us to fight super-elevated versions of the original Wizard City villains. You could create an even more chaotic sense of dread by having enemies appear in the Commons and other traditionally non-enemy areas. To avoid imposing such horrors on new wizards; the attack could be set in an apocalyptic future that requires us to go back in time via a portal (perhaps via the Professor?).
To expand on this idea, it could also be really cool if the premise for this idea was that some new antagonist was attempting to go back in time to critical moments in the first arc to aid Malistaire's plot to awaken the Dragon Titan; thus requiring us to revisit some of the best moments of the first arc.