At least she does know she has some positive traits. ;;
BUT MAN. Okay. Yuuki is.... pretty honest with herself when it comes to her pitfalls. Even if she doesn't like to talk about them aloud. Although she can be a little more harsh on herself.
Yuuki would say that she is pushy, rash, naive, and weak. She feels she's pushed the people she cares about greatly into a corner they couldn't back out of, she realizes that she acts without thinking sometimes, and even then makes the reckless decision often, even knowing it might now always be the best. She gets frustrated over the things she doesn't know, and even when seeking answers seems to find them last, and feels clueless and helpless over what to do regarding those things, causing her to feel weak despite her position.
As for what I was say are her weaknesses....
Co-dependency. She has abandonment issues, and is so terrified of winding up alone, that she does everything and anything she can think of to keep the people she cares about close to her. With Zero she did things that felt caused Zero to depend on her. She wanted him to. And with Kaname, she would dress a certain way, act a certain way, and even leave her hair a certain way to try and please him. She even complied with the whole not leaving the basement rule for over a year because she wanted to keep things happy and peaceful.
I'd also say that she can be-- naive. Sometimes frustratingly so, but also sometimes due to things beyond her power. She also tends to self-blame herself way too much. Much of what happens is not her fault at all in the series, but because much was done to protect her, she feels that if she wasn't born many lives would have been spared/saved.
She also clings too much to the past. Ultimately she mourns Kaname way too long, and even became suicidal after his 'death'.
Has Sebastian ever wanted to make a deal with another character despite his one with Ciel? Whether in canon or Kiseki? Is it possible, or would he ever consider such a thing if it is/were?