I can see the logic of a gaming company using the U-boats, as they went through so many upgrades that it gives more flexibility to the game and allows for more upgrades to the player character's career (i.e. supposed to be more interesting). With American subs, it's mostly a move from S-boats to Gato class and that's it, though hunting in the South China Sea and Sea of Japan was probably one of the most dangerous submarine assignments of the war.
In reality, the U-boat crews suffered a higher casualty rate than any other branch of any other service, Allied or Axis. Of the roughly 1200 U-boats that put to sea, more than 800 were never heard from again. In the end, they lost their war in the Atlantic and were never able to interrupt the flow of war materials to Europe.
America, on the other hand, lost only about 54 of its submarines in the Pacific, and they won the war that Germany could not. Of the 12,000,000 tons of Japanese merchant shipping afloat at the beginning of the war, more than 8,000,000 tons of it was sunk by US Navy Submarines. Naval aviation accounted for another 2,000,000 tons, leaving Japan with only about 1/6 the merchant and tanker capacity it had at the beginning of the war.
The American merchant fleet, by contrast, increased its capacity by several thousand percent.
Odd that no game ever puts one in a Japanese I-Boat hunting American ships though, isn't it?