Many thoughts/questions about all the business of dragon lore presented in Skyrim.
First off, just some things that went down to my understanding
Either during the Dawn era or the late Merethic (I'm thinking the Dawn) the Proto-nords of Tamriel lived in Skyrim. They were subjugated by the rule of The Dragon Cult and the Dragon Priests.

Now was the Dragon Cult and Dragons only present in Skyrim, or was their presence in all of Tamriel, Atmora or even Akavir?

The men had enough of the tyrannical rule and began to rebel, this started the Dragon War. Alduin who is Akatosh and his army dragons (who are also fragments of the Time God) fought men and attempted to eat the world and end the kalpa before the appropriate time. Aided by Kyne, Parthurnaax betrayed Alduin and was the first to teach men how to shout. The three heroes of man created the Dragonrend shout to combat Alduin, this not being enough to defeat him, they used an Elder Scroll to banish him adrift the currents of time.

Ok, so the in-game the Dragonrend shout has the power to simply make dragons land, and defeating Alduin is impossible without Dragonrend. In lore Dragonrend is a shout which makes dragons experience the flow of time like mortals. Now did Dragonrend fracture Alduin's divinity, rendering him a separate mortal dragon that we see in Skyrim? (albeit still a powerful one) After his defeat the fraction of the Time God simply returns to the whole.

After the Dragon War is over, the Proto- men leave Skyrim (maybe some stay?) to settle in Atmora, and perhaps other places such of Akavir. Then, the Nords led by Ysgramor return to Skyrim to drive the snow elves out after the Night of Tears (that's why I figured some might have stayed in Skyrim)

Another thing, ignoring the whole "beast" races of Akavir we know there were men that settled there, maybe they went there after the Dragon War, or perhaps apart of the war took place in Akavir. I'm not quite sure about that at all, were the dragons from Akavir the same as the ones from Tamriel? We know that all dragons were not slain during the war.

Ok, then sorry if this is kind of hard to follow, I'm just trying to make sense of all the different dragon lore. If anyone would like to add anything, or correct something I may have stated wrong please do. I'm trying to get a clear picture. Thank you

The Dragon War is post-Ysgramor, it is believed. Nords came FROM Atmora. The Dragon Cult was present in Atmora, where it was simple nature worship (they worshiped nine animals to be precise- a number that may represent the '8' divines, + Shor)- classical paganism, with Dragons being the top of the hierarchy. The Dragon Cult then became more tyrannical.

Dragons dominated THROUGH the Dragon Cult. When things began to fall apart, they had to get more directly involved, and that's when the Dragon War broke out.

The war was a strictly Tamrielic affair- Atmora was becoming a frozen, terrible place to live, and what remained of the Nords came from Atmora themselves. Akavir, it is unknown why they hated and hunted Dragons, but they did, culminating with the Dragonguard invading and then binding themselves to Reman Cyrodiil.

It is believed that Alduin is much more special. He certainly seems to have a degree of divinity- if Dragons are Angels, then Alduin is an Archangel. Special. It is his DESTINY to eat the world.

The new lore hasn't really been examined or fleshed out to our liking that much. Maybe Beth will rectify that. It is unknown.

Hmmm, I thought it was said somewhere that all the nords were originally from Skyrim, hence the "Return" to Skyrim from Atmora. I thought Ysgramor returned to Skyrim after the Night of Tears to drive out the snow elves. I guess what I'm trying to say is: did the dragon war and the war against the snow elves coincide with each other? or did one happen before the other one?

They could've overlapped somewhat. We know that the war against the Falmer was fully active when the last Dragon Cultists were killed, in the time of King Harald. That was some time after the end of the Dragon War however.

Ah ok thanks, I've also looked into TIL there is a thread about it on the lore forum. Something tells me that the human ancestors of the Blades, even before they became Reman's Dragonguard might of had some part in the Dragon War, because of Alduins Wall and Esbern's knowledge about what is happening. Something no one except for the Greybeards and Parth really know about.

The dragon was predates the Blades by over two thousand years. On the other hand, if the Dragonwar was the Dawn, then the descendants of those who fought against the dragons could have become the Akaviri men who eventually returned to Tamriel and became Blades. Would explain their fascination with finding Dragonborn and killing dragons.

That's what I was thinking, that some of the men who fought in the Dragon War may have wandered into Akavir to eliminate dragons who may have fled after Alduin was banished. Though we won't know for sure, fingers crossed for DLC that expands upon dragons and the dragon war

Oh and I meant ancestors not descendants, hahaha

Could you explain this "it was the Dawn" theory? The game acts like it takes place in the Late Merethic.

Well the Dawn had no linear time, so many of the events were happening at the same time or not at all, so it wouldn't be too far off if mortals viewed it as it happened in the late Merethic. Though did the Merethic happen exactly when Aka's spaceship landed and time became linear?

I take it that the Meritic era happened when time was linear, but it was still quite some time before the 1st and a little jumbled after the Dawn, for that time was all sorts of crazy.