Now, there could be many reasons. But I want to focus on one particular idea that has presented itself to me in the days following the Game Informer release. There are a few things we know now that we didn't know before about the Septim line and about the dragons who have been conspicuously absent from lore. We've also learned a bit about the Dragonborn themselves. And the key to all of this is the new Dragon language that Bethesda notes will be of incredible importance. So, what am I talking about?
Well, the idea is that dragons such as Nafaalilargus, the dragon from Battlespire, and even Akatosh himself may not have been entirely willing servants of the Empire. Now, the only evidence I have atm isn't really worth much. Just a vague female relief image (that some have speculated is Alessia herself) and a game feature that is present in Skyrim. Yeah, not much.
So, I'm wildly assuming that 1) Alessia was a Dragonborn and 2) the Dragonborn, through the Draconic language, can, by calling out a Dragon's true name, enlist a Dragon to fight for them.
Do you think that it is possible that, via a powerful use of the Dragon Language, the Empire seduced a God to be their patron, along with the dragons themselves? Or is a willing union easier to explain?
EDIT: Before anyone says it, I know Akatosh is not a literal dragon.