I guess what bothered me most about her was that she, more than any of the other Animorphs, rang of "Mary Sue." Now, I'm not calling her a full-blooded Mary Sue, because if that were true I would have burned all the books written by her, but she was the most that way of the Animorphs, at least. And, being the roleplayer that I am, anything even slightly Mary Sue just bothers me on some instinctual level. I can't help it, really.
By Mary Sue, I mean that things just seemed to go her way a little too often, the other characters liked her a little too much, etc.
Funny thing is, even though Tobias is my favorite character, I think I can understand why some might not like him. He has a few Gary Stu qualities of his own; the hard life, the 'why me?' attitude, etc. But for some reason, those factors don't bother me so much in his case. I guess because I don't see the other characters bending over backwards to make his life easier like they do for Cassie.
To sum up, basically, like I said before, my dislike of Cassie is more based on my roleplayer-ish instinctual fear of Mary Sues than anything rational. I'm sure if I knew her in real life, as an actual person, I would love her to pieces.