Having Grace Carrow thoughts after this latest reread of twofs and I've finally pinned down what I want to say about her, which is mainly three things: she has a set of beliefs, she's logical, and certain things are inconceivable to her. While these traits aren't necessarily faults, they're emphasized in such a way that makes her appear dislikeable.
First: her beliefs. This includes her belief that everything has a hidden meaning - if the sign says 'do not walk on the grass,' you have to hop being the main example. The main one I think is that she believes in acting in your own interest. She wants to pursue science, so she does. She doesn't see the point in women's suffrage, so she doesn't participate in it.
Second: she's logical, and follows rational courses of thought. Because she wants to pursue science, and getting married (and giving up science) doesn't align with that, she disregards her mother's concern for her future. Because she doesn't see the point of women's suffrage, and therefore she doesn't participate, she avoids those who advocate for it.
Third: certain things are inconceivable to her. She can't conceive of a reason why Matsumoto might be charming, particularly around her, so she chalks it up to his being Matsumoto. It's inconceivable to her that women are capable of making a meaningful political impact, so she doesn't see the point of women's suffrage. But the main thing is that she cannot conceive that people might think differently from her - or, if she can, she cannot conceive how. It's inconceivable that Mori might not be interested in her research on ether, because she is. It's inconceivable then that he might not dislike her like she assumes, and that he's not acting in accordance with some grand plan. Because he knows possibilities and can have plans in place (and indeed does), she doesn't understand why he might let a bomb go off. Mori, like her, is acting in his own interests, but since his (meeting Thaniel and living happily together) don't align with hers, it's hard for her to understand that he is. Similarly it's inconceivable to her that Thaniel can't understand why she's so concerned about Mori, if he is capable of planning around people and making them act as he wants (he is capable, but only inasmuch as it allows for him and Thaniel to be happy).
These things all overlap and intertwine. She believes that Mori is acting in his own interest, which she can only conceive of as controlling events and people for some grand purpose, and she comes to the logical conclusion that he is planning around her and Thaniel (which is not necessarily incorrect, but not in the way that she thinks). She can't conceive that Thaniel doesn't see that Mori is controlling him, even though she understands that he has had a different experience with Mori that leads him to have a different perspective on him. While it's not that she doesn't care about Thaniel, she believes she must act in his interests (cutting down the pear trees, separating him from Mori) until he can. Because of all this she ends up making a bomb and setting it off, because she's logical and she's trying to prove to Thaniel that how Mori is acting is against her and his (joined) best interests. If Mori can stop a bomb from going off, why doesn't he?