In case you're not familiar with it, aquaponics is raising fish and plants together in a symbiotic relationship - I find it pretty fascinating though I don't know all the science behind it. Check it out on wikipedia if you haven't already! I think it could work well with your design ideas. I guess the gameplay would involve having a small set up of two fish and a small row of plants, selling off the plants and the excess fish that are bred. Use money to gain to upgrade components (the tank size, the biofilter, better plants maybe) and increase the size of your business.

If you wanted to get into the business side of things you could also include advertising and market fluctuations. If you want players to have more choices you can vary the fish that they use (common ones are tilapia, crayfish and carp) or the plants (cress, lettuce and kale are common, but tomatoes, peppers and cucumbers are possible) with pros and cons, such as time spent to grow, worth, specific resource requirements etc.

Breeding is a tricky one to figure what the ultimate goal of such a game should be. One that leans towards combat would tread the ground that Critter Mound already does. You could breed to sell (different types worth different amount, demand between types varies), or breed just to "catch 'em all". Genes could happen by chance like Critter Mound, or by using some sort of earned points to buy potential mutations, or maybe a machine that kills x number of creatures to produce one with a specific or randomised gene.

There are various articles on what makes earth habitable that might spark ideas. It needs to be the right size, have a stable magnetic field, have water etc. This could be a matter of a resource-generator creating the molecules you want and balancing the atmosphere, or it could be the earth is already fully formed, you spark the life for single-cell organisms and need to adapt the world to ensure multi-celled organisms can be created, survive and muliply.