To be honest, I didn't find Tobias terribly annoying when I originally read the series. However, I don't remember much of book 3, so that's not a part of my comparison.
What really got on my nerves was the repeated introduction of the Yeerks. It just got old to me around book 20. I mean, it was helpful to me since I started with book 2 and jumped around a bit, but really. After a while, it was just old.