Is an interesting one. Im a little different i think, I think both are very good characters in the series, but I find Nynaeve likeable, and Egwene dislikeable. Interestingly I think in first few books it was more the other way round, but Nynaeve really grew on me, as it became clearer what drives her brash personality, but Egwene's arc made her less and less likeable for me. But both great characters, as both create a string reaction from me, I would say I love Nynaeve and hate Egwene as such.
I think similar for Mat and Perrin for me too, I liked Perrin / disliked Mat early on, but that switched later.
Interstingly think I also have double standards between protagonists and antagonists, being more favorable to the latter / like them more despite similar flaws.