I made myself crazy trying to manage a network of stations with vanilla station-assigned traders and autotraders.
The only way I found of resolving the issues listed in this thread, like stations filling up with unsold wares and trade ships stuck with cargo the station doesn't want, is to reduce drastically the budget of the offending station.
Drop the budget to 10% or 5% of the 'required operating budget' listed by the manager, then most buy wares offers will dry up, and the station will finally concentrate on selling.
Also, that way the stuck trade ships will finally get a chance to sell their wares after a while.
You then boost the budget back up when necessary to replenish supplies.
But it is still far from perfect, which is why I'll advertise my mod, that I made precisely to avoid all that hassle :
Mules and Warehouses.
Set up your Mules once, and watch them handle all the trade for your factories, shipyards, station build storages, and warehouses, quickly, automatically and in the smartest order I could program.