13 did it a bit, but the falcie aren't real gods. They are given power by the real goddess but that was far away and she kind of lost her influence over the world. Or something. The game explains this pretty poorly.

In 13-2, the goddess gives you the power to change history to recreate the true history of the world, but then we are kind of sabotaged by some guy who hates her.

In fact, it might seem like the goddess in FF13 isn't actually both all knowing and all powerful. Maybe she is just one of the things, and just has a lot of the other but not infinitely much.