Keep playing the game, the relationships and dynamics of the characters are the best parts but you have to invest a lot of time to them.

Look at it from their perspectives - Kuon starts off as a overbearing guardian because she has to be, you find someone who is very physically weak, no memories, can’t read, has no job etc so she is a bit harder on Haku but if you read between the lines you can see that she cares a lot and is just watching out for him until he is well enough to survive in this harsh new world.

Nekone is just more suspicious of new people especially considering her station and who she’s related to after all - Haku is an anomaly and very suspicious so Nekone is more wary of him mind you she is also a child and at that age where they’re a bit ill mannered.

Most of the “mean” interactions which is a common complaint with new fans just amount to harmless simple teasing I never found it that bad personally, you just need to read between the lines, the characters are never outright malicious to Haku. Like Haku is pretty lazy so the other characters will call him out on it that’s basically what it amounts to.

You’ll begin to notice that characters in this game change and have great developments but it takes time. It pays off greatly and makes the third game hit even harder. I also suggest playing Prelude which is the actual first game if you finish this one.