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Had Kuja been the final boss, you would have had to kill him. Otherwise, the game would have ended with no one dying which in turn leaves the player confused and feeling as if something was lacking.

It's crucial to the story that Kuja lives and Zidane returns to try and save him. This is symbolic of their brotherhood and how they can overcome past differences and forget about all the problems of Gaia and Terra and their soon-to-be-lost lives. This makes for an especially good ending because now the player can acknowledge that Zidane didn't just mercilessly kill his brother. More than a brother, actually, the only other being on Gaia that's even remotely like him.

Necron was the guardian of the crystal. And after Kuja had done the dirty to it, he had to destroy the world. More specifically, he was going to end all the suffering and pain by just disposing of the universe (I might be getting mixed up with Seymour from FFX, but I'm pretty sure that both villians had this idea in mind)

The bastard was trying to reformat Gaia. xD