One word, incapacitations.

Make fights actually require them and make them part of the battle regimen system when they put it back in. If they planned it well, it could require certain class combinations and get rid of this stupid class stacking. Maybe you need a monk and an archer for the incap, or a drg and blm, or a mnk and drg... the point is if they made it require a combination of two jobs to incap a boss and that incap was actually beneficial, we would be forced to stop class stacking.

P.S.

They would have to make each incap obtainable with more than one class combination otherwise it would completely take away from the players choice of what classes to bring.