The problem, I feel, is that her character progression is tied to the Ala Mhigo part of Stormblood. That entire part of the expansion was pretty badly handled. You leave at level 61 and return at 68. So Lyse spends the whole Doma arc in kind of a holding pattern because more focus is put on Hien and Yotsuyu, and then suddenly has to get all of her growth crammed in at the end. It leaves her without any actual impression of change; she just goes from talking about how she isn't fit to be in charge, to suddenly being in charge, very abruptly. It's jarring.