The last few games and lore pieces have really focused on two of the Aedra: Aka and Lorkhan, the Time Dragon and the Space Serpent. Everyone is paying attention to Lorkhan due to Talos and the Thalmor, but I think this is somewhat of a misdirection.

While it is true that Lorkhan and his plan have been the focus in plenty of obscure texts, it is Aka who is has gotten the attention in the games. The Amulet of Kings was broken in Oblivion. The Septim Empire has fallen. In Skyrim, Alduin and the Dragons returned, along with a Dragonborn. The common thread is Aka.

What reason is there for this? I can only think of two.

1) Aka is trying to get all the pieces of him back into one place, killing the multiple interpretations of him. This could theoretically be done if the Dragonborn hunts down and absorbs the souls of every dragon, consolidating their divine spark into a single being.

Furthermore, Dovahkiin killed Alduin, which released his soul. That may have been taken by Aka, or it could have been a necessary sacrifice to eliminate an aspect of him he didn't want. Then there was breaking of the Amulet of Kings which turned Akatosh into a statue. The falling of Crystal-Like-Law likewise could be seen as destroying Auri-el.

2) Aka is trying to further his influence on Nirn through the return of Dragons, but I doubt this.

Could it be that Aka is trying to eliminate as many versions of him as possible until only the original remains?

There are lots of Aka splinters, and out of the major ones only Alduin is "dead." Akatosh, Aka-Tusk, Auriel, Tosh Raka, Alkosh, Auri-El, whichever Yoku god you feel like equating them with, and possibly Herma-Mora are all up and kickin'. And that's not even considering the various culture gods we don't know of. What Aka do the Sload recognize? What do the Kamal call theirs?

Killing parts of yourself to strengthen your identity is in fact a "metaphysical law" of Tamriel, as I see it. That's why the enantiomorph of Shezarr-Akatosh, and more obviously, a betrayal involved in the Arcturian Heresy presentation of Talos. And why Vivec and Mephala are both gods of duality and murder. So there's precedent for this.

I think what you are closing in on is not so much a thread of the entire series (beyond the enantiomorph, and collapse of divinity in general) as an explanation for the plot of TES 5. But then again, the Dovahkiin might just be cleaning up the shards of the end of the Third Era's stranglehold on draconic myth; or alternatively, participating in the constant conflict of the Dragon God's identity. Killing your opposite self doesn't necessarily make it go away.

Killing pieces of yourself as a cure for insanity? Sheogorath is laughing himself silly right now you guys. He was good friends with Martin after all, he's got a better perspective than many on the machinations of our favorite lobotomite.