In my time playing the game I've noticed something: we are introduced to a new lore element, the Dragon Cult, deeply seated in the middle of everything, but the way it's protrayed is incredibly shallow. There's no books in the game explaining how it worked. Well, ok, there are some explaining the relationship of the draugr and priests, and things like that. But I'm talking about the connection between the cult and the world. What are the DC's buildings: cities, or temples/monasteries? Did they rule the land around them, or were the priests under the jarls rule? More importantly, what about Ysgramor? He's supposed to be this great hero and king, but what was the relationship between the priesthood and him? Did he have to follow whatever the priests said, or were they equals, each of them with their own responsibilities (the king taking care of wordly matters, while the priest dealt with the spiritual needs of the population)? Also, Ysgramor is considered the first historian, who created the first nord writing system. Funny, considering the nords were already using the language of the dragons in their walls. There's the possibility that draconic was considered god's language, and so it could only be used for special occasions. But, again, the game doesn't explain anything.
And about the dragons themselves, how do they fit? The game implies they just passed their time flying and shouting at each other, without paying attention to those little monkeys on the surface. Which doesn't make a lot of sense, considering Paarthurnax mentions dragons have an ingrained "will to dominate", to rule over their inferiors, and that rule took the shape of religion. This kind of totemic religion would work if the dragons were just animals, but once they are intelligent beings the implication here is that, as long as the nords knelt and told them how great and awesome they were, the dragons were satisfied. Pretty swell guys, I'd say. Oh, and their followers were at war with the snow elves, who had a different set of gods (so it's very unlikely they'd accept dragon rule). Did they help them get rid of the white [censored]***? Who knows! Again, no mention anywhere, not even the falmer books introduced in Dawnguard bother explaining it. There's a complete disconnection between the actions of the humans and the dragons.
Finally, there's no real dates for the time the cult ruled, not even aproximations. Just so Bethesda's writers can move it to fit whatever changes to the timeline they decide to introduce.
tl;dr: the Dragon Cult is a neat idea horribly executed. How can we fix it?