Lyse's awkwardness in so many situations, while possibly grating, also made all the sense in the world. She no longer has Papalymo to hide behind as the assertive leader/intellectual type, so she ends up thrust into a leadership role that's completely foreign to her. I think it leaves great opportunity for further character development...or they could use the whole "I'm gonna stay in Ala Mhigo and help rebuild" thing as a means to write her out of the story (without simply killing her off).
One thing I haven't liked, at least through the SB story: all of what, 2 named characters on our side end up dead? As much as I like Gosetsu, him not being dead actually disappointed me...but came as zero surprise since the whole "you never saw the bodies" schtick strikes again.