It's been a while since I've read KOTLC so pls do correct me if I'm wrong.
To me the biggest flaw of Sophie's character is she is a people pleaser at heart. The Black Swan wanted a rebel who takes a stand but years of mental suffering due to her early activated telepathy, makes her shy away from conflict. The Neverseen are easy for her to deal with. They are terrorists who tortured those she loves, most for unclear motivations. There is no pleasing involved. But Sophie's always hesitant to completely go against the Council. Its because of the way she's been raised and all the trauma she's suffered under them. That's why when she dislikes the matchmaking system but she doesn't immediately speak up. That's why she's not super vocal abt her numerous problems with the world, the human conundrum and so on.
Secondly, Sophie is still a child. She is 15. Who is going to take her seriously if she starts going for radical change like overhauling the matchmaking system, the banishment of children, treatment of the Talentless and so on? Not the Black Swan and their Council pleasing asses. She needs time to age and mature before she tackles these topics. She need real world experience. Which she is gaining through the books.
People also say Sophie doesn't care about issues as long as they don't affect her. Sorry to say, the majority of the world is like this. She's too busy dealing with the terrorists actively trying to murk her to think abt it. But when they do affect her and those in her vicinity she realises their effects on the people snd condemns them. (Even if only to herself or her peers) Most revolutionaries are like this. They only realise the scale of injustice once it happens to them and they start opening their eyes to the chains on them and everyone else.
Sophie is changing for the better. What many view as her being rude is her being finally brave enough to challenge the Black Swan and the Council and move against them. The Burning of the Neverseen storehouse is a message and symbol of a more radical Sophie who we will hopefully see more of in book 10.
