For me, convoys have not worked properly since the original Hearts of Iron. In that game you could direct convoys from India to go around the southern end of Africa rather than through the Med where they got shot to pieces. This was done by setting up a convoy from Bombay to a port in East Africa, then to a port in West Africa, then to Britain. You could even divert them to North America before they came to Britain so that all your convoys went to and from the one location (as long as you had enough ships).
The other thing is that they should be units on the map. There shouldn't be any difference between naval transports and transports assigned to convoys. Destroyers and submarines should also be built and sink as individual ships rather than the current flotilla being damaged to 3% of full strength, but then all the ships get repaired. The reality is that if a flotilla of small ships gets down to 3%, most of the ships are on the bottom of the ocean.
