I find it difficult to refute your points, I think Nynaeve vs Egwene is a good comparison to make, they were both exposed to similar situations, both somewhat weathered it and kept true to themselves, however Nynaeve's self was a lot better than Egwene's self.
I still think that I'm not finding Egwene as bad to read as before, but your counterpoints are showing that it isn't necessarily because I judged her too harshly in the past (though I think I still always thought the worst, even in situations where what she did wasn't that bad), maybe she is changing from a character I just hate, to a character I like to hate more, one I can understand better, and accept given what ultimately happens to her (I think if she survived, and remained Amrylin, I would have a different view).
Interestingly, I find Perrin still just as difficult to follow as previously, though at least he did seem to finally 'grow up' (not really right words, but can't find them) in last couple of books, becoming a decent character, but up until that point, boy is it painful reading / listening to....
As I said, Egwene isn't "evil", she's just... Not really all that "nice" or "good" a person, and that tends to rather stand out to a lot of readers because. Well...
Of the main "good guys", and hell most of the minor ones for that matter, she's alone in that respect. A lot of the others do a lot of very not nice things over the course of the books, but with them there's, most of the time, a sense of "they have to do it", with her... More often then not the sense is more "it's more convenient for her".
Of all the characters in the books, and I do mean ALL the characters in the books, the only one who even seems to NOTICE this aspect of her personalty is Rand... And, though it might of played a part in him breaking up with her, he never really seems to give much of a crap about it... Hell, sometimes he even seems to find it funny/endearing.
Mix together a perceived moral failing, with the person in question NEVER, in all of 14 huge books, getting called on said failing... Hell, getting praised for it half the time, and... You've got the makings of a LOT of fan hate.
Still... With all the "observant" people in WoT... How in the bloody Pit of Doom is Rand the ONLY one who seems to ever notice this side of her?