I've been to multiple cities along the Mekong river and never see any type of boats carrying any commercial goods and seldom see any river traffic. I thought this was a major supply route???

there are by far too many rocks, cliffs and shallows in the Mekong River along its course, making  navigating near to impossible for ships with large displacement. Most vessels have flat bottoms, the only way to prevent damage by hidden rocks in the riverbed. 

 

In the recent history, the French did actually think that they could establish a commercial shipping route from the Mekong Delta all the way up to China. Their expansion was stopped by the Mekong Cataracts ( Four Thousand Islands) in todays Southernmost corner of Laos.  They made any passage impossible. 

 

During the dry season, when the water levels fall, you can see all those rocks in the riverbed all along the Mekong which normally are hidden under the waterline during the rainy season

Years back, there were big flat-bottom barges mainly on the Laos side which would carry tons of whole cut trees up river. Some of these had rear cabin accommodation which I heard some foreigners rented for the long, slow ride north I believe as far as Chiang Rai. The most I ever saw was a group of 7 boats, but as I say, some years back. They would rest up at Thakhek in Laos and could be seen from Nakhon Phanom and any northern riverside town.

Now there are 3 bridges with more in the pipeline and some of those trading vessels have been converted to luxury (and very expensive) cruisers. Have not seen any for the past 5 years.