I think you should visit a terminal. The cranes used to load and discharge containers are massive. Often much bigger than any existing vessel as the vessels keep getting bigger. See for instance cranes being shipped on a vessel: http://www.schoonerwoodwind.com/wp-content/uploads/2012/06/c.... Now try and discharge+load e.g. 1000 containers.

In your suggestion did you consider:

  * how would a smaller ship be able to offload a much bigger ship
  * speed of loading+discharging matters a lot and a smaller ship will be much slower
  * where to store the containers
  * impact on transhipment

There are vessels with cranes on them, those are usually not full container ships but more like vessels which mostly handle trucks+cars plus occasional container or breakbulk cargo.

The latest terminal in Rotterdam has switched to working remotely with camera's because it has become impossible to put anyone on a crane, see e.g. following video. Dutch, just look at the monitor screens they're using: http://nos.nl/video/2011857-wereldprimeur-in-rotterdamse-hav...

It's a bit slow and inefficient, and also dangerous to do it at sea. So this is done only if space in the port is at premium.

Which means only Hong Kong still does this: http://en.wikipedia.org/wiki/Mid-stream_operation

It could be done at sea, but it would add too much time and time is extremely valuable with ships this expensive. These ships make money transporting goods, if they aren't moving containers they're losing money.