While it would be cool, the coading would suck.
If it was setup like the trains on a static path always traveling the same route you could set it up like the train, only on water. On the other hand if you make then free roaming/controlable like the CV groups you run into issues. There is a limit to the number of CV groups you can have due to the data involved with the constant up dating of position for the group. Another sea going group would have to fall into those restrictions. Add a merchant fleet, loose a CV group. 
I envisioned it to be set up much like the trains.(Which I want back too.)
Think about it like this: After a long escort mission, the fighters are cut loose on the countryside to wreak havoc on train yards and merchant shipping. I personally get bored after a couple hours in the air and know that the action is over, yet I've still got a few sectors to fly to get home. Please give me a target.
What I was thinking was that every base within a set distance of shore would have X amount of merchant ships and or destroyer pickets attached to it.
They would run a preset course and have no bearing on whether said base could be captured. All they would be there for would be to shoot at us and for us to shoot at them. Perkies would be awarded based on the value that a destroyer holds at the time.
RTBing and running NOE low on the water would be a different animal.