How about soil exhaustion, in the form of a %chance every turn of losing a "special resource" in a worked tile? IT should work exactly as Nuclear winter or heating, but its target would be the special resources, and only them.
It could work like this: every turn, some 1% (or more) chance of losing it, reverting the tile to the same terrain without the special bonus. Maybe the chance could be higher or lower depending on city infrastructures.
On the other hand, each non-worked normal tile could have a minimal chance to gain a special resource, say around 0,1% or less.
This change would have several advantages: a part from realism, it would force players to go for new colonies, it would discourage smallpoxing (althou your cities are small, you may want to let many tiles "resting" around them, hoping they will gain some resource), and it would make more interesting those latitude which usually are not: equatorial and tropics (Desert and jungles), and cold/artics (tundra, glacier) cause they would gain more and more resources as the time pass by, making profitable to build colonies there. Temperate areas would be harmed by continuous exploitation and would become less profitable.