I'd rather have as little need to controll over the micromanagable stuff as possible.
i.e. Have transorts from production site A decide on their own their optimal route to demand site B , but still have to possibility to tell transport from A to B to travel via C if desired.
Will roads be precalculated routes from site A to site B or will there it be civ4 'build per tile' player involved construction?
So that the optimal route will change according to changes to the map.
Personally I prefer an automated pull economy, with some sliders linked to warehouses/armouries to increase/decrease local demands.
Also maybe even economic buildings/workers could autobuild according to demand or availablility of raw materials, certainly people would be attracted to site locations with lots of opportunities. I've loved simulated life/economies in strategy games since powermonger, B&W was also nice. I liked the lack of controll one had in majesty; it would fit with the single character initial stage of the game to have only direct controll over yourself. Controll over production quotas and millitary matters being seconded to subordinates by mandate and various attitude sliders.