The biggest difference is downstream takes less time. Usually there are only a few minor differences for shore excursion programs between ships of the same company and most ships will have exactly the same programs for both downstream and upstream cruises.
 

Upstream means the ship sails against the current from the lower part of the river (such as Wuhan or Yichang) up to the higher part of the river (such as Chongqing). Because they spend more time on board, travellers may get more time for leisure, entertainment and Chinese culture programs and activities.
 

Downstream means the ship sails faster, with the flow, from the upper part of the river (such as Chongqing) to the lower part of the river (such as Wuhan or Yichang). All scenic sites are arranged in the daytime, enough time for shore excursions.