When I was a kid, Cassie was one of my favorite characters, aside from Ax and Tobias. (The only one who has remained one of my favorites is still Ax, though to be honest it's not like I actively dislike any of the characters - though I do have lots of complaints about Cassie.)
The thing is, when I got older and read the stuff, I was constantly stuck wondering this or that about the series. Cassie's an estreen. Okay, we can say she works with animals or that she's more spiritual, etc., etc. Cassie's the only one other than Tobias (who turns out to be Andalite in some strange way, so I guess this could be called forshadowing unless that wasn't planned at the time) who can hear Ax's call under the ocean (Cue blame on morphing powers). Cassie can do morphing anomalies that apparently haven't been duplicated even by Andalites who have done careers like morph-dancing their entire life - and she's never had training in the act of morphing, this talent is au natural. (Well, everyone has a right to be special?) Cassie's a space-time anomaly. Well, I guess anyone can get lucky twice... Cassie is so magnificent and awesome she can get through three missions where she's basically the only useful or present character and still win (Okay, this is getting a little unrealistic.) Any mistake Cassie makes (or risk) turns out to be the benefit and major turning point in the war (What? Really? No real mistakes?). Three of the books are essentially solo-Cassie journeys - The Departure, The Sickness, and whichever one she ends up with Aldrea.
So when I've read as an adult, my problem with Cassie is not that she's human - it's that somehow, unlike the other characters in the series, Cassie always manages to come out looking like an infallible goddess. The other characters, by contrast, have a lot of problems and seem way more human to me...
That, and when I read later on I'd also note things that really bug me. I haven't mentioned my problem with "noble savage" type commentary or "isolated from the world" types of commentary put in either by Cassie or just a general book, but there definitely were a few problems with them.
I could go on, but there's lots of reasons Cassie fell out as one of my favorites.