I think in order to allow units to embark they should have to transit through harbors. It would be more realistic and give harbors more utility. It would also make it easier to defend against seaborne invasions since there will be a limit to the locations an enemy army can embark from instead of every piece of shoreline that currently allows units to embark from. I understand this may not be a popular idea, so perhaps it could be an option players can turn on or off.