I really want to know how it's confirmed that Alduin is Akatosh.
Akatosh can't physically interact with the world and then we have the new information that there was a dragon that was banished from the world because it was on a rampage of destruction. That even strengthens my conviction that Alduin is not Akatosh. The only thing the theory of Alduin is Akatosh runs on is that people believe that Alduin is the Nord name for Akatosh. It's not like the peoples of an ancient civilization have ever misinterpreted anything before... The biggest evidence that it can't be Akatosh is an Aedra, whom can't interact with the world physically. If anything it could be Peryite who slipped into Nirn while the barrier was at it's weakest, which would make more since because it said what allowed for Alduin's return was the Oblivion Crisis.
I believe it's been mentioned by GameInformer but I'd like to think people are able to understand a bit more then that.
When talking about the Aedra you have to keep in mind that they are rather flexible. They're ideas shaped by the perception people have of these ideas. This is most obvious when taking a book like http://www.imperial-library.info/content/morrowind-varieties-faith-empire or the http://www.imperial-library.info/content/morrowind-monomyth. The same story repeats over and over again, with different costumes, music and plots.
Akatosh, Alkosh and Ruptaga all have similar positions. They're all the chief Deity. Alduin is a bit different, he's closer to the Yokudan Satakal, the serpent that eats the world to make room for the new one.
Further more Akatosh and the other Divines are an http://www.imperial-library.info/content/oblivion-shezarr-and-divines.
Based on this it's tempting to think that the ancient Cyrodiils were ignorant. Though that would over look that Akatosh, Alkosh, Ruptaga and Alduin are all the embodiment of time. Though they embody it in different ways, and that difference is best explained by relation between the Nords and Akatosh compared to the rest of Tamriel.
When the world was created the Aedra felt that Lorkhan had betrayed them, or followers of Lorkhan felt that the others were keeping them out of the good bits of Nirn, or Lorkhan was betrayed by his luitenants, or a few other variations on the theme.
Either way the result was a big war. The Nords (or rather their ancestors) had sided with Lorkhan, going up against the Merish hordes of Auriel. So to the Nords Ariel wasn't this glorious god king, rather he was the god of time and destruction come. Hence he - and thus Akatosh - is much easier to associate with Alduin.
You could say that other cultures have repressed this aspect of Time.
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I forgot to address the lack of interaction. Look up, Ama-Nin and John Hawker.
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Is there irony of calling the myths in a fairytale a fairytale?