Please don't flame me on this. I know its rough and that it COULD lead to MM, but I think it has some merit. There are two versions of my model, one simpler than the other.
Anyway, the first is based on the idea of seperating 'Raw' materials from 'manufactured' items-whilst still leaving each GROUP largely abstract.
So, a city will recieve a certain number of 'Raw Produce' (food and 'shields')-based on the number and types of tiles worked, the type of tile improvements on said tiles, player 'input' and citizen specialisation. Most of this generation will happen automatically based on normal player actions.
Under both the FOOD box and the SHIELD box would be a couple of sliders, one will be marked 'Trade', the other would be marked 'Industry'. These sliders would be based on a % system, and would decide what proportion of your food and shields remains in storage, what % ends up in the trade system, and what ends up as 'manufactured', 'processed' and/or 'finished' goods. Any food that gets sent to 'Industry' is available for either 'trade', normal consumption (i.e. just to keep your people fed) or to generate income within the city-via intra-city trade-based on the city's wealth. Shields devoted to industry (after 'multiplication' by industrial improvements and citizen specialisation) can be allocated for either 'trade', 'production' or 'consumption'. Shields left after allocation to 'trade' or 'production' are automatically used for 'consumption'. These shields, like the food, generates income for the city. Also, like raw resources, finished resources are allocated on a % based system.
Now, I understand people may argue this causes micromanagement, but there are a few ways this can be avoided. First, you can assign the duty of divvying up resources to a city governer. Second, you can assign a 'national' allocation through the Empire Management Screen, only going in to specific cities to adjust them to your needs (or just relying on the governer).
Also, to dissuade people from overuse of MM, players should gain increased benefits from leaving allocations in place, wheras each shift of resources should result in a loss of some of those resources-based on the city's corruption levels.

For example, say you have a city with a wealth of 50 (based on size and demographics), whose tiles produce 25 shields and 10 food. Of this, the player allocates 20% to trade, 50% to industry and 30% to storage. This means that 5 'raw' shields and 2 'raw' food go into the central 'trade pool', earning the city money based on its wealth and distance from the capital (though, if the city has a significantly high crime/corruption rate, some of these might be 'lost in transit'). Another 13 shields and 5 food go into industry, with the remainder staying in storage.
The 13 shields which end up in industry get 'multiplied' by industry to form 20 'processed' shields, with the 5 food getting multiplied to 7.
Of the 20 shields, 10% are allocated to trade (earning more money than raw resources), 50% are allocated to 'production' (where they are used to build units and buildings, as well as generate PW points) and the remaining 8 are used for 'consumption', which generates 5 gpt for each shield and food so used (based on 'wealth/10').
Of course, cities of a certain size will need a minimum # of shields/food for 'general consumption', or else happiness will begin to drop.
Anyway, hope that makes sense.

Yours,
Aussie_Lurker.

This might be a good idea, I'm not sure how i would play out, when to trade and when to refine. Will it be a golden formula that will take the decision-making away when you find it?

My point that I'd like to make is - micromanagment is a good thing as long as it involves a level of decision-making that isn't totally negligible for the game's outcome.
It's hard, for me, to tell what outside events would influence your decision on how to manage the produced goods in each city....

Well, the key factors would be the need for 'consumer goods' for your people (which count as 'pseudo-luxuries') the need to build new improvements and units, and the need to generate income for tithing to your national treasury, using to rush improvements and units and even to generate Public Works points. Another issue would be the degree of crime and corruption. For instance, in a corrupt city, you might lose a significant % of your raw and refined goods between the transition points, and crime would cause you to lose a certain % of your consumer goods (and money). At the same time, though, moving things around, a lot, in a corrupt city would cause you to lose more goods each time you change things-thus discouraging excessive MM. So crime and corruption would also influence when, and if, you allocate goods to trade or refinement.
Hope thats cleared everything up.

Yours,
Aussie_Lurker.

I should point out, for the record, that I see this in the broader context of a new population model. In it, you have reasonably 'realistic' city populations, and every tile you work, every improvement you 'man' and every unit you build actually has a 'cost' to your population. For instance, every shield and/or bushel a tile produces, the more of your population you need to devote to working it. As you develop terrain, with mines or farms, you get an increased output, but for about the same-or even less-cost to your population 'pool'.
By the same token, every improvement you build 'consumes' a certain number of your people-specialising them in the process. You can increase the degree of specialisation, but at further cost to your 'unspecialised' population. Lastly, every time you build a unit, it will have a population cost, which you will get back IF you return them and disband the unit in a friendly city. If they are wounded or die, however, you get only a fraction-if any-of the original population back.
What my first two examples would, IMHO, represent is the slow 'urbanization' of the population-as fewer people are required to work in the 'surrounding tiles', but more are required to work within the city itself!
Anyway, hope that makes sense.

Yours,
Aussie_Lurker.