The last few books have all been pretty heavy in topic, even if they've had some "wacky" areas, and this one continues the trend. We see Cassie deal with having to share a mind, two Andalites fighting about how to treat enemies, the return of the Hork-Bajir world and the destruction it's endured, and yet another situation where the kids helped but ended up
Sure, they got the weapons and the Arn now have them in their possession, but they don't free the Hork-Bajir or their world, and in reality they may not ever know how much this aided the situation
Toby wanting to fight the Yeerks on her people's homeworld is understandable and commendable, but it's true she's needed more on Earth, and it's also sort of sweet how Aldrea is worried about her