I think a good mechanic would be for the players to be trying to build habitats and introduce species, while throwing complications at the other players to mess up their habitats. An individual player would build a deck that conformed to specific expectations (i.e. a certain number of habitats, certain number of creatures, certain number of events or problems, etc.) I see this being played along with markers of some sort, so that if you took out a creature from the food chain, the other species that relied on it would have a certain number of turns before they also were affected. Or if the habitat was changed somehow where it would no longer support the species...
I see a player setting up various habitats that perhaps relate to one another - for example, if a lake habitat is played next to a forest habitat, the forest becomes more resistant to the Drought card, or something. Also, animals that can exist in more than one habitat or climate could move to a neighboring habitat if it can support them. Perhaps each player would be limited to a certain number of habitats, or maybe that would just be limited by the number of cards in a deck. A player could have a deck that is stacked toward a specific habitat, or could have a more flexible deck that would allow him to roll with the punches.
Opponents could use cards to introduce invasive species into another player's habitat, or mess with the climate, or just cause some sort of change or disaster. Perhaps a chemical spill could wipe out the algae that support one player's food chain in his lake habitat, starting a chain reaction unless he can clean it up, or introduce another food source. Some cards could be either beneficial or harmful, depending on the context: a rainstorm card could cause a flood in your opponent's Plain's habitat, or it could be used to counteract a Forest Fire.
I also think that it would be important to remember to include humans in this card game. We certainly have a huge impact for good and bad in the world. A City could be one of the habitats, or a Suburb. Human waste, construction, climate change, deforestation: these could all be things that players could use to mess up their opponent's habitats.
This would either be played with a goal to destroy the other player's habitats, or it could be scored every few rounds based on the construction of the habitats, the rarity of the species (some are easier to support than others) and so on, played to a set number of rounds. I prefer the latter as it makes harming the opponent less of an imperative. But a lot could be learned not only in how species interact with each other and their habitats, but also in how events and even small changes can affect the whole environment.
Sorry if this is a repeat of ideas that have been shared before. Like I said, I'm a gamer and a programmer and I think this has great potential. I'm excited to see how this progresses, and I hope I can help out!