Akatosh is a golden dragon. Alduin is (apparently) a black dragon. Auriel isn't a dragon at all. They just happen to occupy the same aedric plane.
While King Edward probably isn't canon after Morrowind (if it ever was, considering how it abruptly devolved from narrative into in-jokes and what appear to be the notes from a dev discussion about metaphysics), some things in it might be. Akatosh was the Dragon God of Time even in Daggerfall (wherein the book was written), yet in the book he seemed to be just a mortal golden dragon, though Mara, Auriel, and so on existed as known and worshipped deities even then. The book described how the dragons retreated from the world because they were opposed to the Aurielic pantheon, though Akatosh was advising them to let go and accept it; he was also actively trying to actively build a small, secluded society where all sapient races were accepted and lived together in harmony. One could argue that the relative racial/ethnic tolerance brought about by the empire and particularly seen in Cyrodiil is the result of his influence on the Empire.
As interesting as the last sections of King Edward are, I only bring it up to point out that if that is canon, then Akatosh was able to mantle Auriel at some point. He didn't replace Auriel, however, he just fulfilled a similar mythic role for humans. However, the plane is the god, so in a certain sense they are now the same being (just like J and S). Because of Akatosh's draconic nature becoming strongly associated with the plane of Time, another less benevolent mortal dragon could have more easily become mythically associated with Akatosh/Auriel and mantled the plane a third time. That is, Alduin would have been a powerful but mortal black dragon at one point, even while Akatosh and Auriel were gods.
What does that suggest? Whatever we end up doing with the mortal dragons, we would pretty much have to succeed where the Marukhati Selective failed to fight Alduin without affecting Auriel and Akatosh in the process. And whatever mechanism we used to do so would represent a risk to every other god, especially the contentious ones like Talos.
This is why I have a problem with the Warp in the West. Yes it tied up the loose ends to Daggerfall but it also set precedent in which whenever there is a gap that needs to be filled with less wild, off-the-handle lore, people move directly back to the Warp in the West and apply it to it. I think it does a disservice to the Elder Scrolls Universe when we go into these crazy scenarios that is characterized by things like some of the information into the Cthulhu Mythos but it fits better in the Cthulhu Mythos. First of all, I really doubt Alduin is Akatosh seeing as how the Aedra cannot interact with Nirn I don't see how he will rise up to destroy the world he helped create. Now it may be a shade or echo of Akatosh as this has precedence with Lorkhan. Lorkhan is dead yet there are echoes of him that show up from time to time. This proves that there can be those that are similar to the Aedra but really aren't them that appear on Nirn because no matter how hard you try, you cannot change the fact that Lorkhan is dead and mutilated. If you don't truly believe he is dead, load up Oblivion, sleep til night time and look up in the sky. See the moons? That's Lorkhan's mutilated body.
Alduin may be some aspect of Akatosh that wishes to destroy what Akatosh finished creating and lost most of his power over. But seeing as how Akatosh and the other Divines can't affect the world, I really don't see how he can destroy it. Also I would like to point out to everyone that keeps citing the Seven fights that they aren't facts, they are tales. Just like in the real world, the tales have some root in reality but for the most part the story has no basis in fact. First of all, I don't think Alduin would be talking to Dagon and a crazy old man while he was eating the world, which is also very unbelievable. Also another thing that disproves this tale as fact is that Nirn hasn't, at this point in lore, be destroyed and rebuilt multiple times. It was an arduous task to build Mundus in the first place, many of the et'Ada gave up their entire beings creating planets, how would Alduin eat the world and make a new one of the same mass as the original when Dagon was hiding pieces of it? Not possible as it would drain him of all his power. "Swallow the world" is most likely a metaphor for destroy it to try to get the power invested in it. And if I'm wrong after all these years of lore research (which I can guarantee I will be wrong on something because no one is perfect) and Alduin is really Akatosh going to destroy the world then surely the Daedra Princes will help stop him seeing as how they are more powerful than the Nine Divines.
As for the dragons leaving Nirn of their own free will, that may be possible for (Golden dragons)? As for the rest of the dragons, the ones in Akavir went extinct and the dragons of Morrowind were massacred by the Cliffrunners.