After reading "http://www.uesp.net/wiki/Skyrim:The_Dragon_War", I had an interesting theory pop into my head...
First, the excerpt that piqued me:
"An ambitious dragon priest, or a particular dragon". Mix those together and who do you get?
Miraak.
I think that Miraak, this mere mortal who somehow had the Thu'um of a dragon, horrified the dragons. Miraak had his little power trip, demonstrating he had the lust for power of a dragon as well. After Vahlok drove him off, the dragons looked upon the mortals with suspicion. How many other of these mortal abominations were there? To prove their loyalty and that they were not like Miraak, the remaining priests doubled down on the despotism. The dragons (most of them at least), eager to avoid another such dragon/human abomination (and because it satisfied that base need for domination) were all too eager to join in, including Alduin. And then the rest is history we already know: The mortals chafing under the tyranny, Paarthurnax deciding he had enough of the madness and empowering the oppressed mortals with the Thu'um, Alduin's banishment, etc.
All because of the first cosmic fluke of a dragon soul ending up inside a mortal coil.