I always saw it as nepotism honestly given who her father is. Conrad specifically says that isn't the case but let's be honest
'because you're you' doesn't hold much water either as a reason when up until that point Lyse hasn't done any leading or shown any qualities that would make her seem a good fit for that role. Of course logistically there was likely a good chunk of her character development that had to be cut to make the first part of the expansion an acceptable length, so for all we know there were going to be instances where she did show she was perfect for the job. It's just if they did exist they never made it into the game.
Honestly I really wonder how different SB would have been if they had broken up the story more and had the liberation take place in a later patch. It would have given Lyse the time she desperately needed to be fleshed out because out of all the issues with that expansion, Lyse really is the character with the most wasted potential. Good on paper but the writing just did her no favors at all.
Which is a shame because has she been written competently she'd have been my favorite character in the expansion. The time she spends in the Steppes really shows growth on her part and I was excited to see where it went... And learning that Ishikawa was in charge of the Steppes content for SB I have to wonder if she had some hand in that. Because Lyse basically had a full character reversal once they went back to Ala Mhigo and it was like someone else was writing her again. Which then only got worse when whomever was in charge of her basically gave up by 4.2 because any outstanding character growth she could have had is abandoned by the time we get back to Ala Mhigo again.