You know, back when Colonization was announced, and before I found out it was a stand alone game and not an expansion. I dreamed that it would add to the "core game"
1) Add a more advanced Economic Model (as mentioned in this thread), as the "core' adjustment (like Espionage was in BTS)
2) New LH Trait (something trade related)
3) Add a few more civs that are were big "colonizers" (Phoenicia) or the product of a colony (Brazil, Mexico)
4) New Trade based units/buildings/wonders. Caravans, Inns, Silk Road
5) A Mod/Scenario that is what the Colonization ended up being.
Anyway, To make it work, the basic function of Colonzation would have to be mimiced.
By this, I mean eliminate resources and the yield, in the sense of what they are in civ, and just change the "Yields" to be the raw materials. Things like Grain ( I dont think there is a need to be too specific), Vegetables, Wood, Iron, Copper, Gold, Silver, Gems, and maybe a few others, which then an be processed by the buildings, creating the "goods", which are then convered into the +

and +

boosts.
For example: You have a Grassland, it produces say 1 grain. have a worker build a specific farm i.e.
a) Grain Farm
or
b) Vegetable Farm
Then inside the city, the grain can be used to
a) Food --> City Grows size
b) Brewery ---> Produce Beer --> Beer sold/traded to other countries for Commerce/Goods --> Commerce is then "procesed" into Gold/Research/Culture/Espionage and the Goods produce more Health/Happiness.
Likewise Vegetables
a) Food (more) This would be the "specialized" thing that just was used to make the cities grow.