I think part of the difficulty with Lyse's character was that she stopped being Yda.
The Ultimate Fight FFXIV video that Square Enix released as a joke during one of the ARR live letters captures the fun of the original Scion group quite nicely. Yda occupied the space where Estinien is right now, as our punch first, ask questions later melee dps. And that served as a good counterpoint to an otherwise overly cerebral Scion group.
Lyse doesn't really have a connection with the Scions, outside of her sister's history. You could argue that, were Yda alive, her sister would be a side character in her story. If you really wanted to bring that dynamic back, then you'd need Yda, not Lyse. The place to look is Yda's implied offscreen/offpage death in Tales from the Twilight - Set with the Sun (as narrated by Fordola):
More and more soldiers were coming to join the fray. She even saw a hulking magitek monstrosity approaching, the grating screech of metal on metal adding to the clamor which now resounded around the ruins.
Fleet of foot as she was, Yda surely could have escaped alone. Yet there she stayed, fighting this impossible battle. She was going to die, and why? For the sake of one child? For her?
Why me?
If she went for help, they might make it in time. But who could she ask? Who would help an enemy of the Empire? No one she knew. She cursed her own uselessness.
Still, she kept moving. One step at a time, though her legs trembled to take them, and repeated Yda's final words to herself until they were a part of her. She would live.
If the Black Wolf came back from the destruction of Praetorium, then you pretty much have to see it to believe it. The question is, if the original Yda was captured and not killed, what could you do with that idea? More of the Resonant plotline with Fordola in Southern Ilsabard perhaps? Bring Yda back as an antagonist? Hard to say, really.