For me, the aliens. The idea that our planet was being destroyed by a secret invasion right under our noses was really compelling. Not to mentioned it explained a lot about my science teacher.
I remember being weirded out by morphing at first -- unsure and almost uncomfortable reading about it. I'm not positive if this was a reflection of Cassie's moral dilemma about where to draw the line, or if it was an unease with the idea of having to eliminate one's body and replace it with a different one in order to be successful.
After the first couple of books, though, I found I perceived the morphing as a really cool and useful tool and, although I was interested in the depiction of the animals' instincts, it was reading about how a few kids formed the Yeerk resistance that snagged me right from the beginning.