It's not like Kuja's soul goal was to destroy the world.

The entire game he is fighting against two things. His own mortality, and his inferiority complex. The reasoning behind his world destruction instinct was the inevitable realization that he could never fulfill his only goals, and the world would inevitably leave him and the memory of him behind.

Kuja was unable to accept his failures. That mixed with his severe Narcisism is what led him to do what he did.

Much better reasonings and motives to do what he did then either Seph or Ulti had I'd say.

Also, Hojo was a real villian. Not the main one no, but I still thought he was a much greater foe then Sephiroth, or most enemies from FF.