Well, in ES, I say Javan Rhinocerous or whatever rhino it was and replace it with the wild bactrian camel (which is endangered, still repetitive, but a new cool animl).
In AA, I say get rid of either barbary ape or gelada (too many monkeys, apes, lemurs, in my opinion..) and put in either a banded mongoose or dwarf mongoose.
In MM2, I say replace the rockhopper penguin (no use having rockhopper without having any other penguins) with some kind of jellyfish.