Wow! This looks fascinating. I had a quick scan of the rules and it looks like you've given it a lot of thought. It'll take a while to read and absorb in more detail, but I'm very interested.
Bring on the trilobites, down with fish.
I've just added ganglia, to try to give insects a more viable path so you may want to download the documents again if you have already.
I'm cheating actual physiology a little here to make the game more interesting while keeping the theme intact: you can have triploblastic creatures without them being bilatarian; and there'll be plenty of functional non-coleomate species running around at the end of the Paleozoic if only because forcing all players to develop all 11 adaptations to become a true tetrapod isn't especially interesting.