Can't find a link for it right now, but one theory I've seen is that the Caucasus Mountains and an Ice Age might have caused the isolation of the gene pools in the first place. Recall that high but normally passable mountains separate the Black Sea on the West and the Caspian to the east. It's a long way around the water barriers if for some reason you can't get over the mountains.
In this scenario, humanity expands north across the Caucasus only to have a population isolated there as Ice Age conditions close the passes. That's the birth of the cold-adapted Neanderthals.
It may be too specific for the available data.
I do find that article rather interesting. I had actually skimmed it once before, but this is the first that I read it.
First, I would very much agree with you that the portrait of Levantine human evolution and also specifically of the relationship between HN and HS in the Levant is much more complicated than that in Europe.
Second, I would reiterate that I don't outright reject the multiregional hypothesis. I do think it has a whole lot of work yet to be done if it is to prevail, but in truth I am agnostic in that regard.
Third, and to be more precise, I do not reject posited admixtures of Homo sapiens and other hominids in either the Levant or in Southeast Asia during the 120,000 B.P. to 85,000 B.P. timeframe; nor do I reject posited multilocus emergence of modern human populations in a zone stretching from East Africa to Southeast Asia. In both case, I am 'agnostic' at this time.
Fourth, and where I think some confusion arises, based on the totality of the evidence to date, and overwhelmingly so, I do reject at this time posited admixture of HS and HN in Europe in the 45,000-30,000 B.P. timeframe.
Speaking more generally, I personally think that at certain points this article appears to flirt with Lamarckism, but I will attribute that to the writing style of the author rather than any of the underlying cited research.
Moreover, I'd be curious to have this placed in a more modern context. Not that 2002 is very long ago at all! But there have been a lot of significant discoveries in just the past 5-6 years and I wonder to what degree they are incorporated here.
But, in short, to reiterate, I do agree that the portrait in the Levant is more complex and more inconclusive. I will also admit that I am less well-versed in areas of hominid evolution other than the Neanderthal/Cro Magnon era in Europe. The latter has sparked my interest more and so I've looked into it in more detail.
And a question you might be able to help out with: Isn't the most recent view that Europeans originated from humans that travelled somewhere over to South or Southeast Asia and then came back over to the Levant and Europe? I might be mistaken in this regard, but that seems to be my vague recollection. I'm gonna have to look that up if you can't help out!