I only discovered this game a week or so ago, and I've been blown away by how good it is. A couple of random thoughts:
There seems be be one loose end. When, quite early on, the MC takes Naomi to that city bar and then finds he doesn't have any money to pay for the drinks, he resolves to come back in a few days and settle up, but he never does unless I've missed something.
If Rae, Caitlin and Lyriel are irritated by Naomi calling them Esha, Lin and El (and we know that Rae doesn't like it and can safely assume that Lyriel doesn't), then they could try giving Naomi some of her own medicine and calling her Omi. That might make her stop, and at the least should lead to some amusing dialogue.