I always liked this concept, reminiscent of FFIV and Chrono Trigger. I'd have the same concerns as Charismatic listed, but I'm sure it could be done generically enough to work...

Instead of:
Flare + Freeze = Antipod (Requires 2 BLMs, yuck)

Do:
Fire IV + Blizzard IV = Antipod (So any combination of BLM, SCH, RDM could create it)

They could of course save a couple uber combos for more specific job combinations. Like maybe Ultima from Holy II + Meteor.