If there is a difference, does the quality increase in the order they fall in the story?
Loot quality actually increases with release date:
What wave you're on, difficulty, and hardcore mode also contribute to loot quality. Note that these are for random drops only; reward qualities are more consistent between levels, but are widely random in quality (i.e. you are just as likely in getting an awesome monkey in Karathiki survival as you are getting an awesome Seahorse in Aquanos).