How about before you can use a resource you need to clear them out of all monsters. Also what about Larger forms of resources such as Small, Reg, Large, Huge.

Small Fire Shard - .5 Resource, guarded by a Minor Fire Elemental

Fire Shard - Gives 1 Resource, Guardian: Fire Elemental

Large Fire Shard - 2 Resource, Guardian: Fire Lord or a Squad of Fire Elementals.

Huge Fire Shard - 5 Resource, Guardian: Fire Drake

This would also apply with Metal deposits, food, ect. It just creates more diversity and more more unique city builds. Along with a reward after clearing out a Mine. Don't ask me what you could do with 5 Fire Shard Resources but the possibilities are pretty much endless at this point.

You could also make very exclusive and rare resources like

Ancient Ruins - 1 Fire, Water, Air, Earth Resource Shard 25% Research 25% Income ect ect. Guardian: Ancient Dragon

I'm a big fan of high risk and reward.

Let me know what you think.