My theory is that the defeat of Alduin would trigger another Dragon Break. Essentially, I suspect we may see TES retconned a bit after Skyrim lol. I could be wrong of course, though. Basically I see three possibilities.
1) We do not defeat Alduin. The world is literally destroyed and recreated. TES is retconned and resets. 2) We do defeat Alduin, but this just eliminates the fatalistic, destroyer facet from whatever Akatosh is. Or 3) We defeat Alduin, and it damages time itself somehow, causing another Dragon Break. TES is retconned but does not reset entirely; it merely redistributes itself so that the time and setting are the same, but the world is somehow changed again, perhaps in such a way that we never stopped the world from being destroyed, but delayed it again somehow.
Hmmm... interesting thought: could the world being eaten and remade be substituted for by a Dragon Break? In a sense, that IS one world ending, and another being created. Perhaps in some metaphysical sense, this temporarily satisfies the nature of Akatosh/Alduin and delays or prevents the destruction of the world for another few millenia?
As for them being one and the same, this is a good example of how divine entities in TES lore are often avataric or archetypal in nature rather than clearly defined or singular in nature.
It has been theorized that gods do in fact gain strength from such things as worship through praise, sacrifice and deed. It may even be theorized that the number of worshipers a given Deity has may reflect on His overall position among the other Gods. This my own conjecture, garnered from the apparent ability of the larger temples to attain blessings and assistance from their God with greater ease than smaller religious institutions.
There are reports of the existence of spirits in our world that have the same capacity to use the actions and deeds of mortals to strengthen themselves as do the Gods. The understanding of the exact nature of such creatures would allow us to understand with more clarity the connection between a Deity and the Deity's worshipers.
The implication of the existence of such spirits leads to the speculation that these spirits may even be capable of raising themselves to the level of a God or Goddess. Motusuo of the Imperial Seminary has suggested that these spirits may be the remains of Gods and Goddesses who through time lost all or most of their following, reverting to their earliest most basic form. Practioners of the Old Ways say that there are no Gods, just greater and lesser spirits. Perhaps it is possible for all three theories to be true.
- from An Overview of Gods and Worship.
That's just one crude, non-specific example, but it demonstrates a clear pattern in TES lore. Deities, or at least aspects of them, are affected by belief and worship. Deities can exist in multiple forms. And more than one interpretation or theory regarding deities can be true simultaneously. So it really isn't contradictory or mutually exclusive to say that Akatosh and Alduin could be one and the same. That's just a part of how TES lore works, both with respect to smaller more defined deities or concepts such as Vivec (who was both a god with extradimensional awareness and virtual immortality in physical form, but also just a man using profane enchantments depending on your perspective,) and grander, less comprehensible ones such as Akatosh being time as well as Alduin the World Eater.