About losing one's humanity...I saw that most strongly with Rachel (who, if you ever read Ishmael Beah's book
Long Way Gone is strikingly similar to how Ishmael was right after his rescue), and with Marco, whose lack of compassion coupled with egotism was turning him VERY much into a little Dukat. Tobias literally lost his humanity, and I think the war really prevented him from getting other kinds of help he really needed. As for Ax, his culture really seemed to have institutionalized that sort of thing, and I did NOT think it was good for them.
Jake...I think he really danced on the line sometimes, but I do not know that I would say he lost his humanity.
Cassie--I certainly don't think she did.
Oh, and in my own fanfic...I don't picture that happening to 7/8, either. Some of that may have been helped by the symbiosis/balancing act that occurred between the two of them, plus I think sometimes dissidence can have a different psychology from defense against an outside force.
I guess part of my dislike for the ending comes from the fact that when we were a few books out from the ending, I'd started writing my own, and frankly, I liked it a lot better. It was the sequel to a prior fanfic I'd written which dealt with an unofficial "Animorph" #7/8 (more like spy).
I would say that Andalite society was not just misogynistic, but also disdainful towards those with disabilities. Couple that with the attitude of their military leadership...and I felt like I was actually seeing the seeds of where the Crayak might be able to make a move on them soon. I had a plot all worked out as to what could happen...and bear in mind this was before I saw the Klingon war arc in DS9, OR the way the Vulcans acted in ENT. I was playing with what would happen if the Yeerk Peace Movement were to gain the upper hand, and basically force a coup. I had this idea where the new leaders petitioned for peace, only for the "Electorate" (swayed heavily by Alloran) refused to believe it out of a combination of hate and arrogance towards the Yeerks and disdain and mistrust of humanity. And at that point, Crayak realizes he's lost his hold over the Yeerks, and so starts making a move on the Andalites instead. I left it with Earth facing the threat of another invasion, with only some VERY uneasy allies (with technology inferred to be behind the Andalites) to hold back the oncoming Andalite fleet.
I REALLY enjoyed that idea, and had it set to be a 4-part book. I still have the outline of books 1-3, and a brief start on an outline for book 4 (which I remember was called
The War for the Stars). No wonder I liked the Klingon-Cardassian arc later in DS9 when I finally got to watch the whole show!

(Not to mention the asshole Vulcans on ENT.)
I felt there were signs in the series that the Andalites were at risk of this sort of thing, but I also didn't think the Animorphs should've all died. (I was also pissed at Marco being rewarded for his behavior.) And I thought it would've been VERY interesting to see Earth deal with such an alien and creepy former enemy in order to prevent their destruction.