That's the problem, usually those who didn't understand why Necron appeared or why SquareEnix bothered putting him in this game end up hating him. But what's there to understand, it's simple we have life and death. Necron is death and the crystal is life, by destroying the crystal what's left.
I guess they could come up with the end where Kuja fails to destroy the crystal, but that would be an epic fail in my book. Why? Well, it seems not many people have noticed but Square Enix had plans for Necron right from the start, the earlier Final Fantasy games showed us the world where crystals were important, they showed what exactly happens if the crystals disappear. The worlds would be thrown into chaos, slowly but surely loosing life. Destroying the crystal in Final Fantasy IX had the same effects, only in this game Necron was the one who would wipe out Gaia if it weren't for Zidane's gang.
As for his difficulty that's completely different problem, it's not just you, many complain about his difficulty which is strange since I found him to be quite easy even on low levels, I suppose you haven't fought Ozma.
It seems you didn't quite understand what Necron really is, as I said he wasn't mastermind as Zeromune and Ultimecia were, he didn't pull the strings which means he wasn't responsible for any of the events during the game, including the mist. He's death itself, and death doesn't appear until life ends, he appeared only when crystal was destroyed just to fulfill his duty.













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