Certainly if multiple copies of a resource had a semi-additive effect on Happiness & Health too, then that might be good. So to extend my earlier example-you have 3 copies of corn in your empire-if, for example, you have 3 cities, then this will generate +3 food & +3 health per city. However, if your empire doubles to 6 cities, then that bonus will drop to +1 food & +1 health, & you lose all benefit if you go to 9 cities. This would better reflect issues of scarcity & force players to either maintain smaller empires or obtain more of the resources they require by war or diplomacy.
Point 2 is this: with strategic resources, demands on the resource from unit building should cut into the supply for the domestic economy. Example-if your 5 units of Iron are generating a bonus of +5 hammers per city, but you go & build 10 swordsmen, then this bonus might drop to only +3 hammers per city. This forces the player to make difficult choices between maintaining a large army & keeping his cities running efficiently.
Point 3 is this: as much as I like Krikkitones idea for resource based trade routes, I do believe that such a system can exist parallel with the one they had in CivIV. i.e. at the start of the game you have only your domestic trade-which will have the smallest monetary value. However this can be boosted depending on (a) population size, (b) being between multiple trading cities & (c) having a resource in your city radius. Then, as you contact foreign nations, some of your domestic routes will become foreign routes. These will be next up in value, & boosted in similar ways to domestic routes. Then you have resource-based trade routes, which will be the most economically valuable-using the formula Krikkitone suggested.
Another interesting idea would be having Social Policies relating to trade impacting on the number & value of trade routes you have, as well as the ratio of foreign to domestic trade routes you have (for example, Mercantile or Protectionist trade policies shouldn't eliminate foreign trade altogether, but should reduce the number of foreign trade routes, per city, by 1. However, it should boost the value of the remaining foreign trade routes-due to tariffs-& probably give a diplomatic penalty to civs you trade with).
Speaking of Social policies, it would be nice to see them effect the extent to which you can adjust certain sliders-sort of like in Civ2 but much more nuanced.
For example-although espionage has been dropped from the core game, if it was still in, then advancing along the Tyranny path might increase the maximum setting of your espionage slider (&/or boost the value of any EP generating activities). Another example is that advancing along the Tradition Slider might actually reduce the maximum setting of your science slider.
Anyway, just some examples to throw out there

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Aussie.