I personally don't have a problem with the way the series ended because it feels realistic. [spoiler]It isn't a happy ending by any stretch of the imagination, but the Animorphs were ultimately successful in stopping the Yeerk invasion, their sacrifices were not in vain, and they receive acknowledgment from all sides for what they did. The surviving Animorphs are finally given a chance to live without killing and making terrible decisions. And if their lives seem hollow after the war, what more could we reasonably expect? They're suffering from PTSD; who wouldn't, in their shoes?
I know the final conflict involving Ax is probably troubling for a lot of readers, too, but it provides a tenuous reason for the Animorphs guys to regroup (which is the best we could expect after all the understandable resentment between Tobias and Jake), and it confirms that their love for their friends is stronger than their anger towards each other.
As for all the loose ends the series leaves, it is sloppy, but I think it's somewhat inevitable in a world this complex, unless the author issues some kind of statement or encyclopedia afterwards. I don't know how many of you are familiar with Into the Woods by Stephen Sondheim, but one of its messages is that life doesn't tie up in nice packages and that there is no such thing as a happily ever after. Life is full of ambiguity, so why should Animorphs be any different? And, as anijen21 pointed out in the loose ends thread, it leaves plenty of fodder for fanfic writers![/spoiler]
My issue, instead, is with Applegate's tone in the letter. A finale so turbulent deserves to be followed by a serious, on-topic note that acknowledges how emotionally weighty and life-changing the last books of the series became. I imagine this was the first time many of us had been exposed to the psychologically damaging nature of being a soldier, especially in regards to children. Doesn't that warrant more than an impossible dismissal and an invitation to join a new adventure?
... Or maybe I'm just unreasonably bitter.