That's my issue with her as well. She had a lot of potential to be frankly amazing given how she was barely even half of a proper character in previous iterations. Yet not only does she suffer in the shadows whilst other characters are given time to shine, what time she does have to shine honestly doesn't feel rightly earned. Oh, we're told she's earned every accolade and the right to our respect. Yet we're shown nothing of the sort, and in fact her characterization during the expansion directly contradicts the narrative the writers were trying to push.
I saw no reason for anyone in the Resistance to allow her to lead, neither before Conrad's death or until the end credits finally rolled across the screen. She was a follower throughout the expansion and she remained a follower at the end; with the pay-off of her emotional growth never actually being written. It feels like up through Othard she had a decent character arc, slowly learning and evolving into someone who could eventually lead the rebellion as we all knew she was going to do. Yet then it feels like they skipped Steps 4-8 out of 10 on how to actually GET her to be that leader, ultimately ending it with 'well Conrad says so because of some contrived reason that makes absolutely no sense. Instead of actually earning the position.'
It also didn't help that portions of her arc were given to Raubahn and Pippin, leaving her with table scraps during the climax. Lyse should have been the one assaulting the city, not Pippin. Lyse should have been the one suggesting the invasion of the civilian quarters, not blinding following Raubahn when they're supposed to be equals. It just left a very sour taste in my mouth. Especially when Zenos was defeated and Lyse strutted across the battlements as if she had /any/ part in what just happened aside from a few minor entanglements. Fighting Fordola does not count, she did that with the WoL. Raiding the civilian quarter does not count, Thancred was arguably more useful in GETTING them through that than anyone else. In the end she was a bit player in her own story when she should have had center stage, and /that's/ what makes me annoyed about the whole situation.