Unfortunately, I don't have the expertise on environmental science to know what is relevant and necessary for human survival beyond the need to clean up and dispose of certain waste products and not to deplete or excessively exploit certain raw material sources. I would try to consult biologists and environmental scientists who specialize in the intersection of human activity and the environment to develop the metrics and possible studies here.
I wont lie I have little knowledge/interest in the other things you mentioned. However, I am fairly interested in the environment, in multiple aspects (as I should be as I'm spending way to much money for a degree so I can work full time instead of summers only).
->Relevant/necessary for human survival
Food. Water. Shelter.
In a more primal sense, what else do we really need? Food/Water are pretty obvious. Shelter being anything from a house or cave to clothing. Computers, cars, even electricity aren't really truly necessary other than we've lived with them for long enough most people can't go without it.
->Clean up and disposal of certain waste products
Pretty much anything we do should be cleaned up. I can't really think of any harmless waste we produce. Even bodily functions are now concentrated so much and mixed with who knows what else that you have something very toxic in the end.
->Deplete/excessive exploitation of "certain" raw material sources.
Sorry I take the keyword here as certain, but realistically any excessive exploitation causes issues. There's only so much mother nature can counteract.
I know I didn't speak towards the game and what could be analyzed as far as it goes, but being that I haven't played it; it becomes more difficult to directly correlate. Personally, I'm probably going to do anything and everything I can to wreck the environment in game, just to see if it reacts as expected or if something weird-er happens.
But back to the real topic. What I'd be interested in seeing more on (and tying back to those three points I took out):
-Species and extinction caused by our interactions (either through over-hunting; specific targeting [i.e. livestock protection]; or just what we do to the environment)
-Recovery of species (can we undo and help a population back to its feet)
-Deforestation and its effects, at that same time how much does our pollution increase due to every player murdering all the trees they can find.
-Mines - really produce multiple levels of pollution when its active its not so much the mine itself but the smelting process that destroys life, after its abandoned improperly you end up with acid mine drainage; water flows through dissolving various substances, direct effect being dropping the pH to more acidic levels (sometimes into the negatives), not much can grow in that but some plants can tolerate a fairly low pH.
To bring people back into it: What do they do to avoid, counter, or mitigate these effects? Which has the "best" outcome? Was there resistance to the restoration projects or did everyone unite to bring it about?
In my mind, its all limited by the software. Does it account for and react as it is known (or suspected) to in real life? Server size/composition - a group of friends on a 10 person server may be fairly similar in their want to keep x around so the spend all their resources to accomplish that goal; a server of 100 people none of them knowing each other there's bound to be resistance. And from a science standpoint, 100 "random" people make a far better study than 10 hand-picked.
Just my thoughts. Should probably go back to trying to sleep again.....