The game will have farming, mining, production of all sorts of gadgets, and the generation and use of massive amounts of magical power. What's missing from almost all games of this sort is the concept that any such activity is almost invariably wasteful, and that discharge of waste to the proverbial "environment" usually leads to the eventual resurfacing of the waste at unforeseen places.
I'm presently working as a chemistry teacher, and this thought was spurred by one of the kid's answer to the question where an up to that point unaccounted electron in a chemical reaction would end up afterwards: "Well, it would go to the environment!" It is a common misconception that there is an environment that can swallow things without limit. I'd find it intriguing if the game could be set up such as to present a reminder to the fact that all things are connected.
For example, have mining, farming, and other manufacturing activities produce waste at a low level, even undetectable, at first. As the complexity of the activities, and the consumption of settlers, rises, it could become perceptible, and start to turn into a small problem. The small problem may be solved by building a landfill at first. That will eventually fill, and a larger landfill is needed some further away from a settlement so as not to reduce growth in the city. After a while, that's full too, or it's leachate kills a forest inhabited by elves who go on the warpath, or the toxic stuff starts generating industrial strength monsters, or whatever, but alternative solutions need to be found. These could be technological or magical. However, no such solution other than full recycling can overcome all restrictions, because, no matter what you do, costs either rise to forbidding levels, or the waste just returns in another form (e.g. incinerated waste returns as athmospherically active CO2, or as fire-breathing dragons).
Same or similar could (should?) go for the generation and use of magical powers. Thinking of a way how magic could create junk, and how to get rid of it, is of course much less limited by real life experiences. E.g. casting a spell could leave behind sort of a charge in the area where the spell was cast, and this charge would repel any magic of like orientation, while attracting opposites. Hence, a former battlefield where massive amounts of one type of magic was used, would henceforth (for some time; effect dissipating/diffusing) be a bad place to attempt to cast a spell of the same orientation, but it would be easier to cast opposite spells. Shards could aid in making the charge dissipate more quickly in their surroundings, or actually add to the charge.
Some people may be turned off by such real world problems impinging on their fantasy world (I'm a god-like hero at least here, Mom makes me take out the trash in real life anyway, leave me alone). Still, I'd like it.