I just finished my reread about a week ago, so I actually feel I can talk about the ending now.
I still did not like it, but I'm finding it easier to accept than the first time. At least it's not going to turn me off to the concept of Animorphs for nine years this time around. It didn't feel right, but I'm not so sure anymore what exactly it was that didn't feel right. I think it might just be related to the ghostwriters' smashing of the characters to one dimension. In the last two books, for example, Rachel almost started to seem like Rachel again- brave, brutal and dark, but still human, possibly with an actual three-dimensional character hiding somewhere in there... and then, it's all snatched away... after all the chaos and the inconsistent characterizations and the uninteresting books... I'm given one more taste of why I fell in love with the series, just as everything goes to hell and everyone gets screwed over...
I don't agree with you guys who are saying it was a remarkably fitting ending. It really sounds like you're just grasping for patterns. It was a bit of a messy ending, and it was supposed to be. Well done, in my opinion, all things considered. I'd still prefer an ending that's more in line with the somewhat unrealistic "survival and hope" message of the rest of the series, but as long as that was being dropped, the Aniending was actually quite good.
As for the post-plot with The One and The Search For Ax... I was actually fairly indifferent. It's no longer the adventure I'd been reading about for the last 64 books, so there's this disconnect there. I liked that the series ends with the beginning of a new adventure... and a world of possibilities...
Side note; does anybody realize that Erek's draining of the Pool Ship's weapons was one of the most illogical things he could have done, based on his programming? Did he know Jake's plan to pit the Pool Ship against the Blade Ship? If he did, he'd realize that a Pool Ship being blown to smithereens would result in a few more casualties than a Blade Ship, even if he believed Jake would vaporize the Blade Ship. Even if he didn't know the Yeerk-against-Yeerk part of the plan, he still knew that the overall plan was for Jake to take control of the ship- would he honestly believe strongly enough that Jake would go around frying every Yeerk on the planet that he'd put the effort into draining the weapons? Even if Jake did fry all the Yeerks, wouldn't that save a far greater number of humans (and dogs), especially now that open war's broken out? Erek's actions sound like he was being resentful and immature, but his programming shouldn't allow that...