This is an interesting question, and one that I've considered before.
I think that KAA is a great writer, and books like THBC, Visser, #26 and #53-54 prove that in particular, because the prose itself is so much more sophisticated. It's as if the further she got into the series, the more free she felt with using more sophisticated language meant for older and/or more experienced readers. Maybe Scholastic also became more comfortable with her using darker stroylines as time went on, too, rather than just providing little tastes of things in the books.
While it was made up as she went along to a certain extent, elements of the stories - such as Marco's mother being Visser One's host, Tobias being trapped in morph, Elfangor being Tobias' father and Ax's brother, Crayak and the Ellimist, "stacking the deck" - and so on illustrate that sophistication and an ability to plan and execute great stories that go above and beyond the idea of children's fiction.
Animorphs certainly isn't perfect, but it's still a great series.