So, it might just be because I'm a bit sick today, that it has somehow altered my mind, but something just struck me...

Isn't Akatosh supposed to be the Alessian Order's mix between Alduin and Auri-El?

Well then, why does the dragons - Paarthurnax and Alduin, for example - call their father / god / whatever Akatosh, and not a third name?

Dragon Break. Basically, the Alessians tried to retcon history and purge Auriel's aspect of Akatosh. They succeeded in at least retconning it such that Akatosh had always existed as the Dragon God of Time, and the Skyrim dragons, being intertwined with Time, no longer remember a time when Akatosh didn't exist. Mortals, on the other hand, are more intertwined with space, and can remember alternate timelines.

There's also the possibility that Aka, as we know him, is actually a Marukhati Selective.