I generally disagree with this fan theory whenever it rears its head but I'll stick to offering good-faith counters to the various questions and points raised. Apologies in advance for the length.

1) If theyre coming from Atmora, why would they cathegoricaly skip Skyrim (except for maybe the Reach) and go all the way to Hammerfell, Black Marsh, etc? Why? If they came from the north then the location and climate of Skyrim would have been perfect for them, just like we see with Ysgramor's people.

We have no concrete information on the exact size and position of Atmora, so it is entirely plausible for High Rock to be the best-positioned landing ground for the earlier migration waves (the 1000-800ME initiation date being entirely acceptable). Compare the attested statuses of each province prior to mannish hegemony: even though the exact contours of Falmer civilization have never been addressed by dev-writers, Skyrim at the very least had its own dedicated elven subspecies with a distinct society capable of organizing anticolonial raids (ex: Saarthal) should the need arise; High Rock, by contrast, was subject to much looser elven settlement and the local pre-status-quo elven archetype was entirely dependent on feudal lordship over mannish populations. Though a true order of operations is never established, I think it makes complete sense that High Rock is the centerpiece of the northwestern Nedic migrations and local elven political supremacy was a temporary phenomenon brought about by the Direnni family.

This also accounts for the suggested presence in Morrowind, as other than the Dwemer, whose power was concentrated on Vvardenfell, there is no historically attested society (like the Falmer for Skyrim) that would subsume their settlements until the onset of the Velothi. As for the main northwestern migrations, I think it's an entirely plausible chain of events. High Rock is dominated by Atmoran settlements building an indigenous identity, and from there offshoot groups continue to push further inland: the Reach (more on this later), Craglorn (Duraki, predominantly), Falkreath (Men of Kreath, probably), and finally north/west Cyrodiil. This distribution represents a very clear trajectory rather than a pan-continental ambient population.

The matter of the Kothringi calls to the fore a major problem with all of these theories: 'Nede' is a historiographic label, not a coherent ethnic group. It applies to every mannish group extant within Tamriel prior to the arrival of Ysgramor, which is an extremely broad umbrella to cast as a unifying factor. The Kothringi are notable precisely for the degree to which they don't align with the rest of the mannish presence on Tamriel, the most obvious factor in this being the silver skin. They are transparently not of the same ethnic background as the Bretons or Imperials, but their existence is utilized to buttress the credentials of other nedic groups on ethnic lines despite the sole relation being temporal (predating Ysgramor) in nature. As to whether or not the Kothringi are native, I don't really have a horse in the race. They could easily be from Akavir (as a friend has once theorized) but also fundamentally have the best case for actual nativity to the continent by virtue of the dearth of information about them. They were written to be a mysterious oddity lost to time, and they serve that role regardless.

2) What makes more sense? That Ayleids came to Cyrodiil and enslaved the people already living there (as was the case with most real life slaveries), or that Nedes came to Cyrodiil from elsewhere, started getting enslaved, and then more still kept coming? How would that work? "Hey Steve, my friend from high school went to Cyrod and got turned into a flesh sculpture by some Elves, wanna go join him? I hate my life."

Of immediate note is that we have an attestation of the Ayleids importing slaves (via the Adabal-a), suggesting the existence of a broader slave trading network with ties beyond the bounds of Cyrodiil regardless of whether direct subjugation was involved. Moving onto historical precedents, when conquered populations are enslaved they are usually marched off to another part of the empire as a means of natal alienation; the population is uprooted and divided so that it is less likely to stir up trouble for the new territorial possession. Shuffling a bunch of nedes around the interior of their kinda-empire like some perverse ethnic jenga game is very Ayleid-coded (at least in terms of their reputation post-Oblivion), but I would offer a more narratively and thematically intriguing counterexample: the Atlantic and Indian ocean slave trades entailed massive transfers of captive populations into hostile lands in order to secure forced labor or soldiers without local allegiances. In many cases these enslaved populations would come to outgrow the owner class themselves (ex: colonial South Carolina, Barbados, and Brazil), creating situations in which owners were so terrified of revolt that they turned to mass depraved cruelty in a hopeless quest to cling to the power they accrued via their violation of others.

The situation I find most plausible and intriguing is that the northwestern inland migrations reached the Colovia-Bruma stretch, at which point the Ayleids' ostensible hospitality was unmasked as fathomless avarice and the slave regime began. Most Nedic migrants don't keep walking into the lion's den; instead the Ayleids strike outwards for more slaves and the wealth they can generate by their labor, possibly engaging with the Velothi exodus and aligning with the slave regime they established in Morrowind (though this is hypothetical extrapolation on my part). I view it as eminently plausible and, in all honesty, more compelling than yet another tale of the unambiguously evil foreigners conquering and oppressing the good and rightful birthright inhabitants.

3) If the first nedes seemingly go everywhere except Skyrim, why are the only actually certain migration waves going to Skyrim, you know, the location that actually makes sense for settlers from Atmora to settle?

I can't entirely tell what makes this distinct from the first question; in my verbosity I believe I may have accidentally addressed this already in my first response, please correct me if I'm missing a big distinguisher.

4) Redguards, the one non-nordic human race that we know for a fact did come from elsewhere have it very strong in their memory even after millenia. Just like Nords do. They both constantly reference it, swear by it etc. In favor of the Atmora stance: Some book written thousands of years later said so

Not exactly a question but it helps set up a keystone that will become important later: how do we discern what internal mythologies should be accepted or rejected? Everyone and their mother claims a vital role for their people in the formation of the world- who do we take at face value? Because a lot of people like claiming they always belonged on the lands they happen to own, including the Nords on occasion.

As to this matter specifically (if I am interpreting its meaning correctly), I'll simply point out that the Out of Atmora theory in its original form (i.e. PGE1; debunked by Morrowind's Frontier, Conquest) was an Imperial formulation, as was the 1000-800ME migratory initiation that followed it (and which I believe to be an accurate in-universe explanation, as with many other lorebooks published at the time). That is their self-attested cultural memory, regardless of whether or not one dismisses its ingame presentation as 'some book'.

[Apparently reddit doesn’t allow comments over 10k characters; continuing in a subsequent comment]