Six seasons and a movie?
I like your setup, in general. But I feel like you've taken out a lot of the most interesting stuff in the first "season" (books 1-13, roughly) and moved them into other seasons - so what's left? I don't know about waiting until the second season to introduce the Chee, Jake's infestation, and especially the subplot with Marco's mom. I've been going back over the early books for my re-read blog, and before Marco found out that his mom was Visser One's host body, he was so. freaking. obnoxious. His mom is his motivation for fighting, and he doesn't find out about her until book five. So we end up with four books of nonstop ****ing about how this is insane and his dad couldn't handle losing him and he'll just do this
one mission, just for Jake, but after that he's out... oh God, I could not handle an entire season of that. Either he has to find out about his mother
very early on or he needs a new motivation to fight the war, which would substantially change his character, so I'd lean toward him finding out even sooner than in the books.
I'm actually okay with leaving out the Ellimist and Crayak. I wonder if the "cure for nothlitism" that Tobias finds could be related to their travels in Z-Space. All their human matter is floating around there while they're in morph, right? Maybe when they're in Z-Space, Tobias finds his old body, just hanging out there, and... wait, no, he'd have to have the morping power to acquire himself again. Well, wait, is there any
good reason why you can't just get the power back from the Escafil device after being nothlited? Maybe once they get the blue box back (although the thing in book 20 where apparently it had just been sitting around the construction site, completely unnoticed by the Yeerks until David happened to pick it up like a year later really annoys me, but that's a whole other story), Tobias regains the power to morph, but he doesn't get to morph back into his old body until he finds it floating in Z-space. Just a thought.
Speaking of nothlits regaining their morphing powers through dubious means, I've been thinking a lot about
The Departure. What do you think about having it take place immediately after the David subplot? Cassie's horrified with herself for manipulating David into trapping himself in rat form, and with Rachel for going through with the plan. It's a good time for her moral discomfort - which has been gradually building throughout the series - to come to a head.
Also, wouldn't it be awesome if the kids had no idea that the Hork-Bajir are gentle, peace-loving creatures? Like, Elfangor explains nothing to them about Taxxons and Hork-Bajir at the construction site. They just see these horrific monsters working for the Yeerks, so they fight them. Then they meet the escaped Hork-Bajir and they're like, "Oh my God, we've been slaughtering these innocent, sentient creatures for like two years without even thinking about it." That would be a nice punch in the gut. Come to think of it, that would also be an appropriate place to put
The Departure. Cassie's stricken with guilt over what they've been doing, and if they've been killing innocents because they didn't know any better, what
else don't they know that's leading them to do horrible things? It also sets that season up with a theme that the enemy is far more complex, and the fight more morally gray, than the kids thought.