I'm not quite sure I understand fully how the game was originally layedout but.....maybe it could be changed based more on a species survival.
Critters further down the food chain would need food therefore the plants they eat would need to be played(like how a pokemon needs an energy card).
Animals further down on the food chain would need to be in play before any larger predators could be played as they'd need a food source(kinda how an evolved pokemon can't be played until its first stage is).
There could be two decks with one being the deck everyone normally draws from while the other could be a "chance" deck which would contain cards that can both help and cripple wildlife (ex.oil spill, national park established). This deck could be drawn from when a player is out of moves or hopeing to draw a lucky card.
Animal cards marked as an invasive species (ex. Brown Rat) could be played by someone to put anouther players card out of the game, but in return it would give other players a chance to play animals that would prey on it.
Maybe there could be seperate decks for each enviroment since it seems hard to cover so many biomes and subjects collectivly. Like a deck for Tundra, Plains, Forests, desert, or reigons Africa, North America, ect. With each deck containing its own animals, plants, parasites, and disasters with each person needing that same deck (ex. like pokemon needs a player to have all one "type" except both players would need to have the same type).
There could be more then one of the same species in each deck. How common a card is could depend on how common the animal is in real life, where on the food chain it lies, and its color(like how some animals have color morphs that could affect thiere survival like white tigers/king cheetah).
Just some ideas, not really sure about the details.