LOL, Vampire Cynthia, so Yuuki's weaknesses is actually a pattern of Hino-san. Were the other manga's as good as VK?
Gosh, am I defending Yuuki?
Yuuki definitely has her flaws but her strength of empathy is real:
(1) she knew to the minute when Zero was going to commit suicide (chapter 4).
(2) (this is a theory) She transformed into a butterfly to stop Kaname before he committed to his plans to the point of no return. The death of Aido-dono was possibly salavagable (it looks like Hanabusa forgave him) but any future moves of Kaname means that there might be no other option for Kaname but to continue on whatever dark path he is on. This might explain Yuuki's desparation at that moment. And why she is not chasing after Kaname now (critical point has already passed)
She has no idea what Kaname's plan is, but she is sensing the magnitude of the situation through emotions only.
(3) She knew when Kaname was serious about killing Zero and stopped Kaname, even though she did not have much blood in her system (chapter 3).
(4) She is one of the few characters in VK who understands that co-existance is the only long-term solution for their world and peace. She is not an intellectual giant, so it has to be from her developed emotional understanding of everyone else.