I think FT got to the heart of it when noting that Rand takes more than enough flak within the books, whereas Egwene seems to be put on a pedestal by her friends and peers - but even more crucially than that, Egwene seems to be put on a pedestal by the writers, and that is what annoys so many readers. The infamous captivity scenes in the White Tower are merely the best example of many - RJ and Sanderson seem to think that they are really displaying Egwene as a kickass heroine, while tons of readers are simply increasingly disgusted, and much the opposite effect is reached of what was intended.
But for all that, she does have her courage, seemingly endless willpower and general competence in her favour, and between that and her status as complete outsider, the argument that she's the best woman for the job is not that hard to make. She'd be a terrible Amyrlin in times when subtlety and the talent of seeing different sides of an issue are required, but those aren't exactly the main job requirements for a Tarmon Gaidon Amyrlin. So the reader, much like the Aes Sedai serving under her, puts up and shuts up about her irritating flaws because her assets are of more importance just then and there.
That seems rather early to be making that call on Egwene - book six is only halfway in her development that will make her so loathed further down the line in books ten to twelve (in particular).
This is a case where she has an opinion on an issue that's relatively familiar ground - her opinions will still be very rigid for some people's tastes, and expressed harshly, but at least they are reasonable enough. It's her opinions on things that are not familiar ground that are more infuriating if you ask me.
And yet Nynaeve is a much more sympathetic character in the end, probably because with her, the stubbornness is usually at least in large part linked to her temper, and her temper tends to flare up most when she feels insecure or afraid. Which is also why she will admit to being wrong sometimes, albeit only long afterwards, and show her softer side. Egwene's stubbornness is much more cold and (supposedly) rational. Her anger is, too, for that matter - where Nynaeve's and Rand's flares hot, hers is ice cold, most of the time. Steven Erikson (the author of the Malazan Empire books) likes to go on and on about "cold iron", a characteristic in some leaders that allows them to push onwards relentlessly and unwaveringly, and pushing or dragging their followers with them, with their eyes on the prize and nothing stopping them. And while I like Tavore or other "cold iron" Malazan characters far more than Egwene, there are certainly similarities.
Agreed.
I don't think there is just one kind of good leader. In leaders, like in most things, it takes all kinds sometimes, and a good leader for one kind of task can be terrible for another kind. One could make a good case that in a largely pre-modern society like the Wheel of Time one, and doubly so in time of war and the possible end of the world approaching, one needs exactly the kind of leaders that we in our democratic free societies of today have come to dislike and suspect.
It's always good to find yourself re-evaluating things like that - rereads would be pretty boring if we always thought exactly the same as the first time around. And especially if so many years have passed and we've changed so much ourselves in that interim, it would be very strange if that were the case.