I'll have to disagree with you on the naval war being over by 1943 (at least in the Atlantic). In 1942-1943 Donitz had enough uboats to start really launching coordinated Wolfpack attacks on convoys, resulting in massive tonnage lost and days long convoy battles. Lots of German resources were dedicated to uboats in 1942-1943.
Granted May 1943 was the worst for the uboat arm, which about 25% of their strength was lost, they were still redeployed to other areas. In game a German player could do something ahistorical and keep pushing the Atlantic War, or withdraw and rebuild...
The Mediterranean theatre was also active during this time period, thought not as much as the Atlantic. Operation Pedestal (1942, during the Rommel campaign), and other convoy operations.
I'd just love if there was a way to strike at Allied supply and slow them down a tad (i guess historically the Germans wished that too), and the Uboat war is the only thing i could think of that could be modeled fairly well in this series.
But i do agree with your take on the Uboat VPs and the historic damage. It is modeled very well, and if that model stayed in game without any additions i wouldn't fuss.