Zergs have been in every MMO. FFXI just took it to the extreme with certain NMs that would wipe you out very fast.

Zergs are fine. FFXI zergs are not fine. If there's optimal classes for a fight, because they inch out another in DPS then something is fundamentally wrong with the content you're making. (I'm aware FFXI isn't the only MMO that suffers from this)

In an ideal world every job would be useful for every fight.

A sub tank to tank adds and DPS once they're handled (WAR).
A main tank who should be able to keep threat on the main beasty whilst dealing decent, but not ground breaking damage (PLD).
A healer (WHM). A spike damage dealer to take down adds or pile up damage fast, with some sort of limiting factor like MP due to the high damage they deal (BLM).
A heavy DD that has no tanking, healing or supporting abilities, but DD's better than the other archetypes (DRG, MNK)
A support who makes everyones job easier, and can support heal in a pinch. (BRD)
A debuffer to keep the mob debilitated, to give the tank and healer an easier job (SMN?)

And whatever else.

On a tangent here, but the main problem is that DRG and MNK both compete for one slot, and they need to fundamentally change one so both can be useful in the same fight.