Honestly, and I'm telling the truth here, I was expecting Rachel to die for a while. Not just because she loves fighting so much she will die doing something stupid; that doesn't contribute to the suspense of the literature. For instance, if Rachel died by randomly being shot by a stray Dracon while flying in eagle morph, it would have been useless and stupid, even though it is actually very realistic and possible. But no, I honestly saw her dying in the war; it seemed to be hinted at in small ways for quite a while. While I was not surprised she was the final casualty, I was still upset nonetheless. If was writing the book, and I was going for the realistic non-sappy ending, I would have done the same thing. Jake can't die, Ax was needed to work on the pool ship, Cassie was too weak, Marco was the key planner and Jake would not let him easily go, and Jake always felt indebted to Tobias ever since the incident were he was captured, and would avoid harm to him at all costs. That leaves Rachel, who gave herself the title of the one who will do anything, even if she didn't feel that way inside. She was the only choice.
I clearly see why Tobias reacted the way he did, and I won't repeat myself because I already said this before in a previous post. When his last tie to humanity was severed, he gave up on it.
Marco did what he would have. Remember, he's the master strategist. He sees moping around would be useless when so much profit could be made. While he is empty inside, he doesn't show it because it doesn't take him the fastest path from A to B. That hidden emptiness, however, is what lets him give up his success so quickly to join Jake.
Ax is the only character's fate I would change slightly. I see him being more depressed than he was in the book. He is Andalite, but he is human inside. Remember, he was only like 13 or 14 by our standards when he started, and still highly impressionable. When he returned to his people, he would be lost. Living just amongst humans would too leave him at loss. I do see him becoming incredibly reckless. His deeds would obviously grant him enormous increases in rank, and I see him making very dangerous choices in bad situations - much like he did. I don't like the assimilation idea though. I would rather him clearly fighting. Even if his fate would still be unknown, I'd want to see more than him simply getting sucked into some random entity. I'd also have Ellimist say something at the end, not to reveal too much, just to have some final statements. I'd still want them to be plunged into a new war, but more clearly. If they are all dead, they can't have a new war, so make the benefit of the doubt a little better.
I see Jake being depressed; the relationship with Cassie was doomed to fail, and this would cause him pain. Also, the war criminal accusations hit him in the heart, because he regretted so many of his actions so much. Flushing the pool ship, bombing the Yeerk pool, subjecting cripples and disabled children to war and death, dooming hundreds of soldiers, he knows that if the Yeerks had done the reciprocal, they would be charged as war criminals, and this makes him feel horrible. Between that and he overall feeling of uselessness post-war, I see him as the sad sack he became, and jumping at the gun to the mission to try to have life return to normal. Return to normal... that's probably the biggest irony of all.