I really don't get how Cassie is the most hated character when Jake doesn't even get interesting until 53 books in, but whatevsies.
Personally, I love Cassie. I love that she's a hypocrite and self-righteous, because flaws are what makes characters interesting. How boring would it be if Rachel wasn't an abrasive action junkie, if Marco wasn't an uncooperative jerk, if Tobias wasn't an angst factory with a martyr complex, if Ax didn't start off unquestioningly loyal to a society that makes crappy decisions? I think a lot of people take exception to the way Cassie is never cussed out by the others, but really, she is, usually by Marco and Rachel. Off the top of my head she gets cussed out in #16, #19, #28, #50 and #52 in fairly significant way. Compare that to, say, Marco, who blows their cover twice and never gets called out for it.
I generally think that the others put up with Cassie's moralizing because they're kids. Kids tend to draw arbitrary lines in the sand as to what is or isn't okay without really thinking about the long-term consequences, and kids tend to lift others onto pedestals and accept their declarations of morals as absolute truths. Especially in a war scenario, they need to feel like at least one of them knows where the line is, so that Cassie can tell the others when they're going too far. So it's not that Cassie's beyond reproach, just that they've set her up to be the good guy, so if they want to play the bad guy and call her out, they've got to have a really good reason. I don't really think that's Cassie's fault so much as the group psychology of the team. As much as they've designated Rachel, and to an extent Marco, as the bad guys, they've also set up Cassie to be the good one, so they can all measure where they fall on a moral scale in relation to each other. To them, the fact that Cassie's still with them stands as a testament to the fact that they're still the good guys - that's why everyone reacts so harshly to her decision to quit in #19, because they not only take it as a betrayal but as her calling them immoral.
Am I making any sense?
Anyway, I think Cassie is probably one of the most accurate to her age range. I feel like she's the one who tends to make the stupid mistakes (1234-5678), shift blame around, act on desperate and well-intentioned impulses (#19, #50), and put short-term goals (not killing, protecting Jake) over long-term successes (winning the war, keeping the morphing box). And it's not like her morals don't shift over the series. Certainly she doesn't get a big dramatic shift like Ax's "I betray the Andalites!" or Jake's sending James' people to die, but she does start going along with more and more morally questionable things. I mean, in #43 she refuses to blow up the Yeerk Pool. In #52, she's one of the people riding the subway on in.
I MEAN WHATEVER. TEAM CASSIE YO.