One of the reasons I liked the series is that as it progresses, it shows us how nothing in life is black and white, good and evil. Originally, the Yeerks, Taxxons and even the Hork-Bajir (to a lesser extent) are portrayed as the evil bad guys that we have to wipe out.
However, book 13 is proof that the Hork-Bajir are in fact a peaceful race enslaved by the Yeerks. Book 19 shows us that not even all the Yeerks are evil, as some of them refuse to take hosts. The Andalite chronicles then tells us that some of the Taxxons resisted their hunger and Yeerk rule.