First: I'm not 100% sure how the prices for ordinary goods work today, but it seems the prices are rather fixed. I suggest altering these prices to a "supply and demand" system.
First, determine the base demand of each good in a port. I say the base demand should be proportional to the population, to increase the incentive for large populations.
Then, prices are adjusted every day based on the supply the previous day. If the supply was higher than the demand, a minimum price is set (a price that will still give a small profit). If the supply was less than, say, 10% of the demand, a maximum price is set (maybe 10 gold above the minimum price, maybe twice the minimum price). If the supply was somewhere between 10% and 100%, an appropriate price is set (maybe lower it by 1 gold for each 10% of the demand that is met).
Why do this? Well, as it is, traders will always prefer "short" trading routes, since there is very little to gain from longer routes. With prices set based on demand, one can probably make a profit even selling tools to Akrotiri. This will lead to more diverse trade routes. It will also make for competition and cooperation when it comes to trade routes - a guild will make sure not everyone uses the same trade route, since that would decrease the profit.