In a thread about an earlier prehistoric era I mentioned that if a resource was used to intensely, whether it was one of the Wildlife resources or just one of the Plant resources, it could disappear for awhile (in the case of plant resources) or in the case of a Wildlife resource migrate to a different tile (random direction, terrain permitting and up to three tiles away) which would make the hunter/gatherer unit that the thread was about have to move every so often to be able to re-harvest the tile.
From the get-go the Wildlife resources should migrate occasionally until the tile is properly developed with a camp or pasture. And definitely the fishing resources! Geez, don't even get me started on that one..
No question, in a 'dynamic map' model, which is what I want, some 'natural' resources are going to move on their own. Migration of fish, animals, sea or land resources could even be linked to a more game-long Climate Change Model, in which the Mini-Cycles of climate over the last 6000 years are included in the game, so that Tundra changes to Ice or Plains/Grasslands, Deserts expand or contract, and, of course, that would 'push' Deer, Elephants, Cattle, Horses, Sheep, etc to 'seek better pastures' unless you've already penned 'em up.
Part of this also would be to have some Extra Special Places. Like the Grand Banks shoals of fish off the New England coast, or the Humboldt Current off South America, where resources of certain types are so concentrated it becomes a Natural Wonder - to be exploited if you can get to it.
on manufactured resources
Without wanting to change anything you've already mentioned (because dayum dude, you nailed it!)
what I do feel that's missing are Gunpowder, Munitions and Fuel as mid-late game added manufactured resources.
Gunpowder would be made by combining (Niter + Coal) in a Gunpowder workshop that replaces the regular workshop. It creates a number of Barrels of Gunpowder per turn, and slightly less production.
Munitions are made by combining (Gunpowder- either already made or just the raw niter and coal + Copper) in a Munitions Plant that replaces the regular factory, and creates a number of Cases of Munitions per turn, but no added production.
Niter is an 'artificial' resource, since most of it has Always been manufactured: Nitraries or, in the 20th century, in Haber-Process Chemical Plants. Charcoal. likewise, has always been manufactured by burning forests, a few trees at a time. A Gunpowder Plant, then, would just need a forest tile or two within the city radius (which your 'charcoal burners' would have a High Chance of depleting into Plains if they kept at it long enough) and Nitrarie smelling up the Neighborhood. For an added bonus, a Gunpowder Plant could have a 'Nuclear Power Plant' mechanism where it might explode violently due to carelessness, possibly taking out a Building in your city.
Munitions: I do NOT want to make a game out of "Build your own Industrial Complex In Order to Have a Military". Counting the repetitions in old wallpaper would be more interesting, IMHO.
Also, 'Munitions' by sheer volume and weight, are not all equally important. Artillery ammunition has always represented by far the largest percentage of munitions, (like, in a WWII infantry division, the basic load of artillery ammunition weighed 9 times more than all the infantry, machine-gun. mortar ammunition combined). And the biggest component of artillery ammunition is not the explosive filler, it's the shell bodies and casings - made of steel. Copper is important only for certain types of ammunition, but artillery ammunition sucked up between 1/4 and 1/3 of all steel used by the belligerents in WWII (well, the major belligerents: USSR, Germany, USA, Britain). That's a Huge Industrial burden, which the game currently ignores.
However, that burden, strictly speaking, only becomes important in the Modern Era. In the Russo-Japanese War of 1904-05, the armies shot off up to 200 - 400,000 rounds of artillery in a battle. By the Balkan War of 1912, it was up to a million rounds a month. By the middle of WWI, the British army alone fired off over 3,000,000 rounds of artillery ammunition in a single two-week period. And, unlike the artillery pieces themselves, you have to keep manufacturing ammunition continuously as long as you intend to actually use those guns.
So, if we're going to model gunpowder (and 'smokeless powder' that replaced it at the end of the Industrial Era) and Ammunition/Munitions, then I suggest we keep it simple: model artillery ammunition, increasingly required by all units in the Modern Era and on, and the 'raw material' for it would be Steel and Nitrates (explosive).
Fuel is refined from crude oil at a given ratio like one barrel of Oil gives two barrels of Fuel, and that ratio can be improved upon with later technological upgrades (like the way farms give more food with certain break through technologies and or civics). The Refinery doesn't replace the factory this time, it's a new district that has to be either next to an Industrial- or a Harbor District for adjacency bonuses to kick in, and also comes with it's own three tiers of buildings.
Crude Oil Storage Tanks could be added, and upgraded to Fuel Storage Tanks which covers the highway fuel costs for the city and surrounding region more efficiently.
High Octane Refinement could be another add on, making the highway maintenance the cheapest a player can achieve (outside of separate automotive developments), or a bio fuel refinement process facility that uses food instead of oil to produce Fuel
Plastics Production Facility as the last inclusion to the refinery.
The problem with a separate Refinery complex/District, is that the earliest Refining was done right at or near the Well - and still is conducted very close to it, in places like Russian Baku, USA Houston, etc. Let's not directly model the entire process, but instead allow Upgrades as a result of Technologies that add 'extra' Fuel from your Oil because of discoveries in engine manufacture, gasoline additives, etc.
High Octane Fuel I want to keep as a potential Upgrade for aircraft (Want to expand the Giant Debt Robot's technology Upgrades to ALL units in the game eventually), allowing them to get better combat factors, better range, etc.
Special ability (I shun to say special powers...) would be that a city can have two refineries (within regular district allowances)
Downside to this thing is that it tanks the appeal in all directions.. what was that you wrote? 'stomach churning disgust?' Sounds about right.. so having two refineries in a city means you want it to look like Pittsburgh, and don't deny it..
I grew up near Pittsburgh: it was the coal-smoke belching Steel Mills that turned the city into Black Skies 'R Us in the first half of the 20th century, not Oil refining. But you're on to something: Pollution should be a game-long mechanism, ranging from burning coal to heat cities ('London Fogs' in the Industrial Era) to Oil and Steel production or simple concentrations of Factories from the Industrial Era on.
The way that I thought that units could utilize the Fuel and Munitions (and Gunpowder) resources would be if they only consumed Fuel resources when they were actually moving, not including when they're moving over Railroads, because those resources were already 'paid' for when they were built.
Melee units would need both Fuel and Munitions for attacking, since they occupy the tile when they defeat an enemy.
Cavalry units (helicopters and tanks) would have an extra 50% Fuel usage, but only when attacking. That goes for naval units as well, ranged or melee, them boats use a lotta fuel
Ranged units would need either Fuel to move, or Munitions to fight, but neither at the same time.
Planes require Fuel for everything, because those sucker ain't exactly known for being fuel efficient..
Spec ops units would require Fuel for paradrop incursions, and use extra munitions during attacks and while defending, because those boys just don't know the meaning of semi auto

No fuel requirements when they're just huffing it through the bush though..
To give a few figures, since I've been delving recently into a lot of German and Soviet WWII archive documents for a book:
A Panzer Division required twice as much fuel as a motorized infantry division to move the same distance,
Aircraft engines required two-three times as much fuel as the same number or tank engines, and up to 10 times the fuel of the same number of truck/wheeled vehicle engines.
Any unit armed largely with small arms, no matter how trigger happy, will use about 1/10 as much ammunition by weight as a unit with an artillery component.
And in the scale of the game, Even if a unit is 'standing still' it's going to be running vehicles and engines.
So, Munitions would be required for anything 'Heavy': Battleships, Aircraft Carriers, Tanks, Artillery, Rocket Artillery, - they will all fire off ammunition by the 100s of tons. Infantry, Recon, 'light' ranged like machine-guns or antitank direct fire weapons - really don't require that much weight of ammunition by comparison. No matter how hard they try, they just can't use the tonnage that the 'heavy' units can - unless they melt every barrel and launch tube in the unit.
All Modern Era and later units have vehicles - even a German infantry division in WWII, which had over 3000 horses (in 1941) also had up to 500 trucks and cars. (By comparison, a Panzer Division in 1941 had over 3000 motor vehicles). So Every Melee, Ranged, Anti-Cav, 'Cav' (tank/modern armor/helicopter) unit will require Fuel BUT tank. modern armor, helicopter units will require twice the fuel, and air units 3 times the fuel per turn to do anything. Recon units stay useful because they represent fewer men, more lightly equipped, and so compared to everybody else don't require any continuous resources of ammunition tonnage or fuel by the cubic meter..
Here's an added 'tactical' touch: if a unit expends extra fuel per turn, it can move +1 tile per turn - the good old 'day and night' pursuit or road march, which unless you are sitting on Fuel supplies stacked high and wide, you can't do very often or with too many units.
Railroads should be followed by Highways so that a player can get away from coal altogether if they so chose (and railroads that travel through areas where a city is producing sufficient power, should have an electric cost, not a coal cost). Highways would have a Fuel cost per turn, which would be reduced by automotive improvements developed yourself, or imported through trade with others.
Highways would eventually be replaced by Hyperloop transports, because Elon needs all the positive reinforcement that he can get. Can only be built between two cities, with further development it can be laid out in coastal waters and later upgraded to be laid out in ocean tiles. The cities pay the electrical cost to run the hyperloop line split between them.
Travel through city districts would be like through tunnels, instant teleport at a fraction of the movement costs.
Actually, by the Atomic Era (1940s) virtually all railroads were burning Oil, not coal - they'd converted to diesel-electric locomotives. Change the graphics and add Hyper Loop later, but the Railroad can transition seamlessly to highway or 'modern' railroads and either one will require a new fuel source.
And, for certain, railroad tunnels and later communications tunnels should be buildable under Coastal Tiles in the Atomic and later Era - Chunnel is only one of several examples in the world today.
For the corporations I would say that other civs (player included) can start a competitor corporation, but only after a branch office has been set up in one of your own cities.. and those copied corporations would always be a little less productive than the corporation founded by a great person.
I do think that the competitor companies ought to have names like units and rock bands.
Like Rock Bands, I'd give them 'basic' game-generated names but allow free renaming by players. Any Corporation with "Acme" in the title would, of course, have a chance of any of their installations, buildings, etc. Exploding on any given turn . . .
Speaking of farms (were we?), a late game introduction could be bio-fuels which use food resources to create Fuel resources.
Speaking even more on farms, greenhouse tile improvements (upgraded from farm improvements) ought to be a thing that cities can build anywhere as long as it's flat, making tundras and deserts more useful.
Near future upgrades after greenhouses would be warehouse hydroponic systems (replaces the factory) and the vertical farming towers that science is currently looking into (can be built pretty much on any tile, on hills, flat lands, whatever..)
Again, 'farm' improvements can also be moved backwards in time. Right now, the game makes virtually no use of the Irrigation Tech at all, yet the various forms of Irrigation could have a huge effect on farm production.
Early Irrigation with dams (take out that artificial Great Bath monstrosity and replace it with the Mar'ib Dam, one of the earliest Flood-abatement/irrigation structures in history!) should make it possible to 'farm' plains and desert tiles near a river or even up to a tile or two away from the river (qanat systems of ancient Indus and Afghanistan watered areas hundreds of miles from the water source). Modern mechanized irrigation pumps and sprayers allow just about any part of the desert to be farmed, and combined with Bio-engineered plants, massive increases in production from each irrigated 'tile'.
And some plants have had 'Production' bonuses attached to them for a long time: using your grain or rice to manufacture Distilled Liquor as an Amenity/Trade item ever since the Renaissance Era, for example.
Bio-Mass for Bio-Fuels can theoretically be anything, but, again, Bio-Engineered plants will probably be the best bet in the 'near Future Era'.
A Tech or Civics advance could also allow City Farming - roadside, abandoned lot, Greenhouse Rooftop and other areas converted to 'agriculture'. It would have both a Food Production (perhaps simply 'modeled' as a % Increase in Population Growth) and possible Amenity component, and even a Green Revolution/Sustainablility mechanic with it. This sort of thing is gaining quite a bit of traction in the cities here in the Pacific Northwest where I live, but it's been done in Western Europe since the mid Twentieth century in various forms.
Whew! Lot's of things to play with. Thank you very much for your Input and ideas.