Necron's place as the final boss was in of itself an important throw back to the old Final Fantasy games.

If you look at the clear bookended theatre references you will see that Final Fantasy IX draws a lot from theatre which can be didactic at times. Hence the monologues.

The scene with Zidane running through the Iifa tree is clearly badly done but that should not detract from anything. When did graphics have an effect on the storyline, hmm?