First, i think the charges against the two captains are to set an example and as a warning to others.
It would also appear to hide the facts that far more senior officers up the chain of command, all the way from Annapolis to the Far East fleet have been negligent.
While flying military aircraft we had a problem with CRM, crew resource management, ie, someone of junior rank being afraid to criticize a more senior person - this may explain why not one person on the bridge did not question what was not happening to avoid a collision, assuming anyone on the bridge had enough awareness to realize that the ship was in imminent danger. In my dealings with the USN this is indeed a problem.
Basic training for watch personnel is obviously lacking - this should be an easy fix, the other problems are more difficult.