Surprised nobody has talked about 14 yet.
I don't mind books with limited connection to the story arch as long as the story within them is interesting. Lots of these books deal with isolated and somewhat isolated missions that don't advance the overall picture much.
But book 14 was a 100 and some page long farce that built up to an alien toilet joke....
Whenever I re-read the series as a kid I always sped through #14. It was the only one I did that to. Not interesting at all. When I re-read the series earlier this year I was reminded why.
Personally, though, I don't understand this need for various fandoms recently to trash "filler" like some piece of diseased meat. I also think the word "filler" is overused and misunderstood, especially with a series like Animorphs.
Animorphs is and always was a series of commercial children's books. Each book was designed to do nothing more than appeal to children and sell well. There was not some grand overarching plot intricately planned from the very beginning that the series played out (until the end, anyway). There may have been some ideas, but nothing laid out as concrete groundwork. As such, each book was just meant to be a fun adventure involving animals and aliens and kids. Some books were better than others. Some were referenced more often later on. However, I think its ignorant to dismiss everything else as nothing more than "filler" just because it didn't advance some un-existant grand scheme.