Sure it's far too late in the day to raise this but, IMHO, naval warfare would best be handled in a similar way to the war in the air. So you could still have actual units representing naval groups, but as well as moving and individually targeting opposing units, they could also remain in harbour but be set to the appropriate range for the scale of the scenario, and - like aircraft at present - on a setting of 'Interdiction' or 'Naval Superiority' or whatever sounds appropriate.
They would obviously have to be limited to striking targets on sea hexes, not land. This would mean in a large-scale game such as 'Europe Aflame' the British Mediterranean Fleet sitting in Alexandria (or Malta, Gibraltar, etc) would be set to 'Interdiction', and would have a chance of striking an Italian fleet or embarked land unit moving through the Mediterranean. This would be better for large-scale scenarios than the current system whereby you have to physically move the fleet unit adjacent, or almost adjacent, to an enemy fleet in order to engage it.
It would not preclude moving the fleet unit adjacent to an enemy one, nor prevent it being physically moved adjacent to a coast to be used for shore bombardment, but would allow for greater flexibility in naval warfare. I'm not an IT man, but the mechanics must be there as air units on interdiction do it all the time, very realistically.
As I say, probably a bit too late to suggest this now!