Without disk for this game would feel very unfinished for me. Sure you kill Garland in disk three, but Kuja is still a big enemy.

And considering the party couldn't defeat Kuja, ever, (it more or less appears during the last fight he toys with you, I mean him not using Ultima right away doesn't make sense :P) it wouldn't make sense if the party just crushed him right away.

In fact, I loved that the party got humiliated there, it really but a sense of "woah" in Kuja's power. Also, Kuja's motive of wanting to kill everything. I thought that reaction was most fitting to his character. Over and over Kuja is shown as selfish, and selfloving, when he finds out he's got a designated time-limit to life, I thought his, "If I can't live then no one can!" Attitude completely fit his character.