I've been very fascinated by the story of this game and I think it isn't as flawed as some people claim it is. The game suffers from poor storytelling yes, needing Datalogs entries and offical guides to fully explain it self but the more I think about it, the more I realise how clever the story is put together.
Anyway, most people are too lazy to read through the Analects (which I think are a lot of fun) which explain pretty much everything. I noticed there is a lot of confusing about certain plot points in the game, one of them is about the Gods, specifically the Maker known as Pulse.
Some people claim (s)he is the goddes Etro (I believe the FF wiki claims this), and others say it is the creator of Cocoon, Lindzei. I think both of these suggestion are false.
If we take a look at the analects we learn that there are several gods: Luminous (Etro) the goddes of death, Stout (dunno?) the creator of the world, Sage (dunno?) the creator of magic(?), Fool (Lindzei), and the Maker, creator of both humans and fal'Cie. This already proves that neither Etro or Lindzei are the Maker, and that he thus is a totally sperate entity.
The goddes who intefered twice during XIII's storyline is Etro, and not the Maker, though she is refered to as Her Providence. This is once again proven when reading the Analects.
...so I hope the storyline makes a little bit more sense nowHer Providence sought nothing.
Her Providence made nothing.
She but looked on, silent in Her sorrow.
The Goddess pitied mortals, destined as they were to die, and so She deigned to intervene in the hour of their greatest peril. She averted cataclysm that was to be, and put to rest the ones who would have robbed so many of what time fate had ordained.
Her compassion did not end at this.
The Goddess pitied also those subjected to that fate of Focus, crueler still than death. To them She sent Her messengers, to deliver hope when all was lost.
If there is anything else that isn't clear/doesn't make sense then I love to take a look at the problem and try to explain.