The Skirt Na actually seemed to be making fun of the little green men cliche, which is why they only showed up once imo. The Andalites were created to break that cliche.
Saying that though, the biggest cliche to me
are the Andalites. Not by their physical appearance (that's actually pretty original), but the fact that they seemed like saints and saviours at first, only for us to find out later on about their arrogance and their double sided objectives.
The Yeerks themselves were also a cliche, seeming all evil at first, and then tugging our heart-strings by revealing to us of their circumstances. Most of the series was cliched as well, right down to the individual Animorphs.
Jake: The all good american hero
Marco: The comical specialist
Ax: the foreign informant/outsider,
Cassie: the pacifist
Rachel: the girl power, tough as nails character.
Then there's also Visser Three, which is like the complete collection of every stereotypical bad guy out there (was there ever actually any sort of depth to him, other than wanting more power?
)