Well, Necron... I said my points about him already, but maybe I might add some of my own theories?

Necron appeared right after Trance Kuja destroyed the Crystal, source of all life and existence. I've always imagined that Necron was sealed in teh crystal, it's exact counterpart.

Think about it, Necron is destruction, The Crystal is the bringer of Existence.

Inside teh crystal, Necron saw all of Trance Kuja's actions and made his own conclusion about it all: Kuja wanted a total destroyed world, so he would not be alone in death. Necron concluded: All life desires a world where there is no pain, or suffering, or all the other problems life brings.

Teh crystal was destroyed and Necron came free. His mind was set on his ultimate and only goal: give life what they desired. A world without all those problems caused by life. How? By destroying every existence, where there no longer could be a crystal to give life and suffering.

You can't call that random. He had a goal and that goal was caused by Kuja's actions. Some sort of chain reaction. NEcron can be seen as a better worked out version of NeoExDeath (which is logic, they even use the same smurfing attack, Grand Cross).
So, random? Don't think so.

Now, teh place where you fight him... That's a harder cookie.
Well, I see it like this, and I think it kinda makes sense.

Trance Kuja destroyed teh crystal with his all powerful Ultima. I think such an immensly powerful attack could easily destroy the ground our characters stood on.
Trance Kuja destroyed the crystal world and we saw him fall. It would be nothing more but logic if our characters fell with him. And where tehy landed was the Hill of Despair, with Necron's 'colloseum' up in the smoke of the fires (or clouds, whatever) around them.

It would make sense if the Hill of Despair was below the Crystal World. How else would Kuja have teleported Zidane and the otehrs to safety after the battle? So Kuja was somewhere on or below the Hill of Despair as well.

Conclusion: Necron fitted in the storyline completely and not random. His actions were caused by Kuja and so was his freedom. Can you call that random? Sure, it was unexpected that he came, but not random.

Also, you could have guessed Trance Kuja was not the end. He's too un-Final-Bossish for it. He's too small and not very impressive, ya know. He could not be the Final Boss. Making him transform again would kill the story and making his trance form more impressive would have spoiled the Final Boss form on the end of the 3 disc.

So, please stop complaining about Necron. This post may be completely wrong, but if you look it through my way, you can see some logic, I think. Trance Kuja had a great soundtrack, but it was also not very Final-Bossish, and his background was not very Final-Bossish as well. Necron had a great battle theme as well, less cool than 'The Dark Messenger', but still great and surely fitting the last battle. My only complaint was Necron's background. I found it not very Final-Bossish. I think a cross between Zeromus and NeoExDeath's background would have suited him better.