Nynaeve makes a great Queen for Malkier imo because they are respectful to authority, unlike Two Rivers or Emond's Field folk. She is kind of a warrior. It's ok for men to be gruff and take no shit from people, but because Nynaeve is a woman she has to be soft and kind? Egwene wasn't soft and kind, she was arrogant and selfish. Nynaeve and Egwene are not like Perrin. Egwene rose to leadership by gaining acceptance of the other Aes Sedai... Nynaeve doesn't care about gaining anyone's acceptance. So much so that she'd choose Lan over being Aes Sedai. Not many people are like Perrin btw. Perhaps not anyone. All of our leaders are kind of aholes except Perrin and Elayne.

Not all leaders are liked or make friends with people. Some people lead with an iron fist, which is early Nynaeve, thanks to the stubborn people she dealt with in Emond's Field. Nynaeve has had leadership skills the whole series. It was Nynaeve, as early as book 2, that leads the rescue of Egwene. It's also mentioned she's good at politics... when it matters. She just doesn't care to be patient with people. She is rough with others and herself. Over the series, she learns to accept herself and others, which turns her into a better leader, but I bet she still brooks no non-sense.