I've more or less forgotten the bad parts- the sometimes ridiculous or contrived plots, the minor plot holes that were ignored by the next book (remember how in one of the later books, they found a crippled Andalite just living in their neighborhood?), the varying quality of the ghostwriters.

Instead, my memory focuses on the AWESOME concept, the incredibly dark tone (especially for what was ostensibly a young adult series), the memorable characters, and the interesting alien creatures.