I think food trade should be automated. This is how.
Players can assign a percentage of each city's food surplus to the national pool. This is controlled on a nationwide basis as a slider ("each city assigns X% of surplus food to the pool"). Pool assigned food is first reduced based on city corruption and efficiency of transport technology. Until you have rails and hermetically sealed transportable grain silos, transporting food just isn't going to be particularly efficient.
Next, surplus food is assigned to any cities that have a food shortage. If there is not enough to cover all the food shortages, it is assigned to cities according to culture. The higher culture cities get their shortage met before the lower culture cities.
If any food from the pool is left over after all cities have their shortages met, it is assigned to all cities proportionately according to the total culture in each city. Say you have 1000 total culture, 500 in your capital, and 30 surplus pool food, 15 of that pool will be sent to your capital. This reflects that the breadbasket plains 'cities' of the midwest don't grow, but the cultural centres on the coast are massive. It also prevents a serious MM problem.