Her arrogance and hypocrisy know no bounds
These books had a lot of the instances that used to really get to me regarding Egwene, especially with respect to Rand (both her generally thinking the worst all the time, and the hypocrisy she tends to portray around what she is allowed to do and what she believes Rand should be allowed to do).
I very much agree with your last point about her progress here on out basically being gifted by the opposition - given her and Siuan's thoughts around having Nicola quietly removed, I'm really surprised that Elaida didn't just execute her, especially once she started receiving feedback on what Egwene was doing.