Okay first part. Toll Taxing, I believe cities should have toll taxes. To get rid of a toll tax from a certain city you\'ll have to complete a quest. Just like in spoonscape.
Second Part. Okay each geographical location should have a scarcity in certain types of goods that will allow a better use of \"traders\" someone who trades things for money or for rare items that trade and so on...
For example if you have a city in a desert water and fruits/vegetables should be rare therefore more expensive than in a city in a jungle. But the desert city would have more mining, where as maybe the jungle is not as minable as the desert.
Cold areas would have more monster/animal furs while a city would have more synth textiles. So the animal furs would sell well in a city where as the synth textiles would sell a bit better in the cold area. etc...
And so on, vice versa...