1. This is the first book where we see Jake contemplating that he might need to destroy his brother, Tom. How do you think KA handled this? How do his thoughts now compare to later on in the series?
I think it was handled pretty realistically, and seeing as how I never got past book 24 or 25, I can't really answer the second part of that.
2. What do you think about the Yeerk himself and how he acts. For example, do you think its realistic of a Yeerk to give himself up so easily (when he sees Ax)? Similarly, do you think Ax should be able to discern a non-Controller from a Controller as well as he did?
Andalites are the Universe's experts on Yeerks, so yeah, if anyone could tell easily, it'd be an Andalite. And as was stated, it really wasn't that hard. As for the yeerk itself, it's only a lower-level Yeerk. Not all Yeerks are expected to be as calculated as Visser 3.
3. In this book Jake doesn't act as if he has any reservations about parboiling a couple hundred Yeerks, but later on he seems hesitant. Most notably in #54 when he flushes the Yeerks from the ship. Why do you think he had a change of heart?
By that point, he's understanding everything a lot better, not everything is as simple as black and white.
4. Why do you think KA decided to introduce Crayak in this book? Especially since he isn't really mentioned again until...I think #26?
A nice teaser.
As for another question, what do you think Elfangor would have thought of Jake for flushing all those Yeerks, when he was willing to fight Alloran to the death to STOP him from doing pretty much the exact same thing?