I wish there was a game which would get the physical foundations right* so that the ecology could be put on as a topping. What I imagine is something like a Civilization, where each map cell would be like 1 km2 and you could define what industries would be in that cell (perhaps even design the content of each cell). Each cell would contain a little piece of civilization and/or nature. These cells would then exchange different materials with each other, according to conservation laws.
That could be used to educationally model ecology very nicely.
Most games of this type will focus on military and/or logistical challenges of civilization. But this game would focus on production chains, land/resource use and sustainability.
(*IMHO, the way to get the physical foundations right is to do proper accounting of materials. So in the game, you never really ever destroy anything, you just transform it. If you need to round a number for some reason, then it would become part of some global pool of "waste", from which it could be later retrieved by some industrial process.)