The biggest missed opportunity in the game, now that I think about it, was not tapping into the mythology enough. Someone in your party should have become a Cie'th and you would have to fight them. The fal'Cie should have spent less time focusing on the L'Cie and more time harping on about his ultimate intention, to bring the gods back. The other fal'Cie should have had a voice as well as Barthy. Orphan should not have been the end boss. The ending should have been discussed at some point in a "We've been Ragnarok before, what if we could control ourselves and use Ragnarok against Barthy?" kind of way. There should have been a lot of this kind of thing. Generally, the wider plot and the mythology of the gods/fal'Cie/l'Cie/Cie'th should have been far more ingrained into the storyline and every part of the process explored.