It wouldn't be the first game where resources run out and the only remaining one if wood. In this game it would be: "Time to go back to stones and sticks." Consider it an incentive to go to war.
You have an ecosystem with some mines already discovered of various types plus some still undiscovered. For now lets forget about the Channeler and friends.
In this scenario, my dear Winty faces Toadboy in a game. Soon in it, Winty takes control of an iron mine near her city. Once the mine structure is built (the same you would build a farm for food), automatically one of her citizens is sent as miner. Mines, as any other building you have, needs population to work and these have a minimum and maximum of population that can be used. Lets say that Winty's iron mine allows between one miner and nine miners. As long as there is at least one miner, the iron mine will produce 1 iron ore.
If by any reason Winty decides that she wants more iron ore production, she would only need to send more miners to it. In this case, lets say that Winty's iron mine (Mines of Loria) admits between 1 and 9 miners and that for each 2 miners above the first, its production is increased by 1 (making up numbers, don't take them too seriously). If she has enough population she could order her advisor to send 8 new miner to Mines of Loria for a total iron ore production of 5 each turn. If later Winty had to recall 3 miners for the army, leaving 5 miners there, Mines of Loria would produce 3 iron ore each turn.
As technology/science advance, Winty can decide to promote one of the miners into an engineer (making up names...). Or maybe recruit one from the proper building (the same building that allows you to construct/recruit catapults may as well let you produce some engineers). The engineer increases production of the mine by 1. Because of balance (perfect excuse to put caps on things), lets say that only 1 engineer in each mine. That ingeneer doesn't only increase your extraction rate a bit, he also has an cummulative % of discovering new veins of mineral in that same mine. So if Mines of Loria has a iron deposit of 1000, yourengineer may eventually find an extra 250 iron deposit for it. All mines would have a minimum and maximum number of times that this "event" could happen. Maybe a mine in the plains would have between 0 and 1 but a mine in the mountains could have between 3 and 6. This engineers can also do some sightseeing out there and discover new mines in other lands.
There could be different kinds of mines and not just about their base resource. Maybe they need a minimum of 2 miners to produce 1 ore each turn because of a difficult location but it's the only Mithril mine in miles that you control. Or maybe because of location, the mine produces 2 ores each turn with just 1 miner.
Later, Winty sends 3 more miners to Mines of Loria, having now a production of 6 iron ores each turn. Some turns later, Winty's civilization makes a new discovery and improves mining techniques, increasing every iron mine's production by 2. Those new techniques also allow Winty to extract ore from adamantium mines, which always come in handy.
We don't truly need quality in our ores so scrap it.
So the game continues and suddenly Toadboy notices something. Winty controls most part of the iron mines. Her military isn't the best (lazy ass diplomacy dependant Winty) and toadboy's iron reserves are still good but... well, in the long run she has all the advantage because if the game drags and he cannot take her out, in the end he will be the one that will start using stones and sticks sooner. What to do? Maybe trade as much iron as possible to increase the reserves. But that's expensive and doesn't solve the problem. What then? Obviously... war!!
Just some random ideas, don't sue me.
