One thing that's interesting is that if you played 1.0 and started in Gridania, then you met the original Yda. 1.0 had players time travel into the past a lot with the echo beyond just cutscenes. The echo flashbacks were 10-15 years into the past, so Lyse would have still been a child.

Another reason for the switcheroo is that by having Lyse not be a Archon, that gives her more reason to be able to stay behind in Ala Mhigo and for the narrative to focus on a smaller set of characters for Shadowbringers.