Its mentioned many times, several by Kellhus himself, that he picked Esmenet as a likely breeding vessel due to her intellect. The 'native intellect' is also mentioned a few times.
While I am sure that Kellhus believes that is a good way to discover breeding potential, I doubt if it is intellect at the foremost of why Esmenet can carry his children and none other can.
I agree, I always thought that the intellect thing was one of the conditions required for a worldborn woman to be able to bear half-Dûnyain children. It makes them more likely to succeed than those without that "native intellect", but there's something more.
In another thread I mentioned Maithanet's mother and Cnaiür's mother, both of which were also able to give birth to non-deformed half-Dûnyain children (mostly guesswork on Cnaiür's mother here, but her child seems to have been killed just because she was Moënghus', there's nothing to make us think that she might have been deformed like the "nameless ones"). If we knew more about both of these women, maybe we could figure out something that both of them and Esmenet had in common?
Yup, that's probably the case, but we don't have any information, and at this point, anyone expecting some kind of future text revelations isn't paying attention.
I always suspected that something that creats the difficulty has to do with the Nonman blood, and that the dunyain genetics program was selecting for those genes. So to me, perhaps there's some nonman genetic stock in the at-large population that smooths conception for dunayin-worldborn hybrids.
No idea about Cnaiur's mother, but she gave birth to Cnaiur, and he's arguably one of, if not the, most intelligent worldborn to exist in recent history. So, one might expect his mother to have favorable 'native intelligence', or whatever, for good hybrind dunyain breeding stock.
As for Esmenet and Maithanet's mother, I would guess that they have, somewhere in their ancestory, the bastard child of an Anasurimbor, and therefore, that nonmen genetic stock. Often people describe those with interesting or different persectives than themselves as 'intelligent'. We know the Nonmen have an alien POV regarding many things, perhaps this is what gives the illusion and or vague descriptor of 'intelligence' when describing those exhibiting similar alien thought patterns.