OK heres my 2 cents,this is going to be vast so i'll break it down.
resorces-this should be a simlpe shield set up tiles would read 10 shields ,20 shields ,30 shields all variable but in incraments of ten to keep it simple, these are raw goods,oil ,grain,silk,etc.. and finshed goods ,food, armor,ammo,cloth etc..there are 3 basic types of these resorce/shields.
1-growth.should include high capacity grain ex-wheat.low copacity grain. ex-corn .high cappacity meat, ex-cows ,wild meats-game,low capacity fish-exe-crab,medium capacity fish exe-shellfish,domesticated fish exe-fish
2production-should be broken down into 3 catagorys-building material,ie clay,stone,hard wood,steel and aluminium.building capacity,this should be population shields and beast of burden shields.ie horses and cow.supply shields,food ,iron,oil,coal and uranium.
3luxurie this is the simplest of all.
how to collect these resorces is this,everything should be in shield form including population, say 10 shields for every population ,these shields along with beast of burden shields carry out the grunt work for the civ,building improvements, collecting resorces, building , supplieing millitary and so on .In collecting of resorces every resorce shield should require a population shield or beast of burden to collect it ,this could be an automatic thing in much the same way it is now,but the shields are neccesary( i'll explain down the road). To increase the amoant of a resorce that is being collected you should have improvements that you can continue to add to each improvemaent adding a 10% increase in collection.ex-A tile outside of city A has 10 shields of iron .you would have to allocate 10 population shields to harvest all 10 shileds ,now you add a mine .the amount of required population shields to collect the iron decrease to 9 .add another mine and it decreases again to 8 and so on.of course to make it ballanced your going to have to have a maintanance cost on every improvement,thats the job of cottages and towns.
to move the resorces the road network and trade needs to change.first i think that you should have more than just a road that connects to be able to collect that resorce,there should be stages of road ,each increasing the amount of resorce that can be moved.back to city A: your collecting 10 shields of iron from your iron tile and the city is connected by a levl 1 road (each level should be able to move 10 shields per turn)city A also has 2 other iron tiles ,each with 10 shields .they are also connected to the city with a level one road. now you have 30 iron shields in city A.to move these shields in total to your capitol would require a level 3 ( for 30 shields) road.obviosly to be able to trade with other nations, is going to require building up of a road network or trade network..to handle trade on coastal cities, ports should handle this and should be treated as the same as roads .each port you build in a city increases your export/import capacity by 10,there is a point i want to make about supply on this but later.
how to use the resorces-first of all tiles that dont have resorces should have 3 basic shields :clay for grassland and plains, hard woods for forest/jungle and stone for hills .All improvements should require a raw good and a prodution amount (raw goods would be building matreial shields and production would be population shields)ex. a foundry should require 5 stone shields or 5 hard wood shields and 15 production shields. outside of building basic millitary,science,and gold, all improvemnts should be for increasing the capacity of shields.ex.city A has 30 iron in the city ,build a foundry and now you icrease your capacity by 50% ,now CityA is producing 45 shields of iron.
back to building the foundry,you have 3 population in your city(30 shields)cityB is collecting 20 stone and is connected to the capitol by level 2 road. that means you have accass to 20 stone in city A(every resorce should use the road indapently ,all resorces go into a general slush fund and roads are the limits on how much a city can import/ export)each iron tile has 3 mines on it (keep in mind that every improvement decreases your population needs by 10%) which would only require 7 of the 10 population shields to collect the resorce ,meaning there are 3 population shields left over on each tile .those shields go back to the city and become your production shields or hammers as we know them in civ 4,meaning that the 9 production shields(3 from each mine) will take 2 turns to build the foundry that requires 15 shields ,with 3 shields left over for the next turn.
for units this should require x amount of population shields and x amount of building material shields. Most units should have a supply shiled attached to them and used every turn ex. legions should have a food shield that they need to be supplied with that is automaticly taken out of the slush at the begining of the turn,rather than stopping the unit if supply is cut it should have collateral damage applied to it every turn. some units having higher % of collateral than others.units that run on fuel should have the highest% ,while foot units the lowest.the amount that that can be supplied depends on the road the unit it is traveling on ,a level 1 road can supply up to 10 shields,because units that require fuel along with food will require more supply shields ,you wont be able to move large amounts of armor in enemy terratory unless thier trade network is built up .as for navy ,your ports should determine when your navy is out of supply ,this should aslo work for trade,each port level should grant one tile of supply . in other words a level 3 port would mean that your gally can move 3 tiles out from the city before it begins to recieve collateral damage .as for trade it should be 3 tiles for every level of the port.this is the base level and as techs increase the amaont of tiles for port level would increase.
I have much more than this but ill put this out for now.
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