Based on the facts that we know,it could be that Alduin is actually Akatosh.
We know the following facts:
1.Akatosh is a dragon.
2.Alduin is a dragon
3.The only ones capable of fighting dragons,are the dragonborns.
4.Alduin was alive and animate in the past,and he just "froze" at an uknown time,until the conditions of the prophecy are fullfilled.
5.Tiber Septim was a dragon born,killed a dragon.lit the dragonfires and became emperor.
6.The heirs of Tiber where too dragonborns,even Martin.
7.Since Tiber Septim Akatosh is the protector (?) of the empire.
8.It was Martin's will that he merged with Akatosh to destroy the Prince of Destruction,meaning that Septims have some power over Akatosh. (since they can call him to fight for them whenever they want)
9.The prophecy says that after the Oblivion gates open,a civil war will wreck the empire and then Alduin will come back.
10.When the Oblivion gates closed,the Amulet of Kings was destroyed,and there wasn't any other dragonborn of the Septim familly left.
So,my theory says that perhaps the dragon that Tiber Septim neutralized was Alduin,and Alduin's body was left at stasis somewhere while his spirit was trapped by Tiber Septim.
And since Septim have his soul and he is a dragonborn he can command or control to some point Alduin's powerful soul.
Tiber Septim might used Alduin's soul for good purposes,and thus making the dragon's doings be good.
But that doesn't mean that Alduin's soul is following orders with it's own will.
Perhaps after several generations word of mouth was spread that the Royal Family has a dragon protecting them,and the empire.
Through centuries,history was distorted and Alduin's soul became known as Akatosh a supposed "Good dragon god that protects the empire".
But what if the amulet of Kings was the container of Alduin's soul,working as a soul gem ?
And with it broken,and no more Septims the "curse" broke and Alduin's soul was able to return to it's body.
Now Alduin reanimates himself wanting revenge.
The mortality/divinity thing is always a little unclear with Aedra. There are some not-quite-canonical implications that Akatosh himself was a mortal golden dragon that ascended to godhood just as Tiber Septim, but by becoming one with Auriel rather than a new god. Alduin could have done the same to Akatosh.
We don't really know how Alduin can be manifest on Mundus. The lore is pretty vague on this point -- on the one hand, Aedra don't tend to directly involve themselves in mortal affairs in the way that Daedra do, presumably since their energies are largely directed at preserving the natural and social order of Mundus. On other hand, if they've decided to destroy the world, that will probably no longer be a concern. It could also be that the lore was deliberately misleading, and that the lack of aedric intervention was due to some sort of restraint imposed on them from the mortal world.
Tiber Septim's antics in Skyrim have always been something of a mystery, one which will probably be unraveled a bit in Skyrim. However, his ascension to godhood is almost certainly tied more directly to Numidium and the Underking than Alduin and Akatosh (incidentally, in real world mythology, Talos was a giant made of bronze). Only certain people were capable of controlling the Numidium -- like the amulet of kings, it may have only responded to dragonborn. Mannimarco was able to use it to kinda sorta ascend to godhood, and it has some ties to Lorkhan, insofar as it was originally created as a vessel for his heart.
Martin was able to call on and merge with Akatosh because the Amulet of Kings contained a portion of Akatosh's power -- though I imagine only a dragonborn could use the Amulet such a fashion. However, it's not clear whether the Amulet was a gift from Akatosh as a symbol of a covenant (the straightforward pro-Imperial view), or a portion of his essence stolen by the Shezzarine, perhaps in retaliation for the betrayal of Lorkhan and theft of
his divine spark (the subversive view). If the latter case, it may explain the (relative) lack of aedric involvement in the world since the Amulet's creation. That is, removing Lorkhan's divine spark from Red Mountain made it possible to open the doors to Oblivion; so perhaps removing Akatosh's divine spark from White Gold Tower will make the return of the aedra to Mundus possible (that would suggest there is some aedric anologue for the Dragonfires that would be holding them back even in the absence of the stone from the tower). But I'm just speculating.