Interesting to see that this subject brought a lot of interest and some very informative comments.
Just one thing,if you are to develop Short Sea Shipping, don't look at modifying existing ships, or using tugs and barges, especially as Container feeders. Start building up a fleet of highly efficient and economical vessels that can actually do the job safely and efficiently.
Modern Short Sea Vessels come in many forms and sizes, as can be seen in Europe and Japan, among other places.
There is no need to re-invent what has already been developed, tested and proven elsewhere. I'm sure that naval architects would be happy to introduce their models on the US market.
Damen, Rolls-Royce Marine (UT design)and others have long experience in supplying design and equipment packets to shipyards world wide. There is no reason why that couldn't be the case for US yards to build vessels to the Jones Act for a future US Short Sea market. (Except national pride maybe?)
You should also remember that "Short seas" doesn't only mean domestic USA. Add on Canada, the Caribbean and the northern parts of South America to the equation.
Ships like Damen's Combi Coasters could pick up cargo at Inland Ports along the major rivers and bring it to anywhere within the CONUS or beyond. (Incl. Inland Ports in other river systems)
Fully developed there should be a small number of Hub Container Ports in or near CONUS, able to handle the largest ships of the future, with feeder service to/from smaller ports along the coasts and inland waterways + "Dry Ports" at Railway junctions in states without access to navigable rivers, or the sea.
Some of the feeder vessels must be able to handle both sea and river transport to avoid transshipping more than one time.
Some must have cranes to load/discharge unaided in ports without suitable facilities.
The major secondary ports may be served by larger gearless feeders, while still be classed as "short sea" for regulatory purposes.
Would this be possible? Yes,it is already reality in other parts of the world.
Will it become reality in the US in our lifetime? Maybe, but only if attitudes, rules and working habits are changed with it. You cannot have a traditional "gang" of Longshoremen watch each fully automated crane and autonomous transporters do their work. Even lashing/unlashing will soon be done with minimal human involvement.
Somebody has to stuff/unstuff the containers though, but that will not likely be done in the Ports, or by Longshoremen at their present wages.