31 is it for me. The one where Tom's Yeerk has to be away from the pool, and we find out apparently the Yeerks don't have any contengincy plan for Yeerks needing to travel. What shouldn't be a big deal winds up driving a whole plot because Tom's Yeerk acts like an idiot. Also Jake didn't attempt to rescue him. Granted this isn't handing his brother over on a silver platter, but you have a situation where Tom's Yeerk leaves, and none of his people expect him back alive. So end the Yeerk, fake Tom's death because what Yeerk would be suspicious of an involuntary controller committing suicide, and Jake's main goal in the war is complete.
I don't like Reverand Cassie either, but I'd rather read about BuffaChapman again than 31. I might put 54 as my worst too, but part of the problem with 54 has to do with the final arc in general, so I single out 31 as the plot that just should not have happened.
I agree 37 didn't do Rachel's character justice, but the opinion the authors have with rachel in general doesn't seem to mesh with what I gather from most of her narrated books anyway.