Excellent post! I am more familiar with the U-boats than American boats because I played SH3 for quite a while, used the mods, and used the Type VII and Type IX extensively. I learned how to turn the boat into an agent of terror against my enemies, and even through '44 make it a haunting specter that may yet rise up and snatch an unwary merchant beneath the depths.
One reason I wasn't familiar on American boats is because I just got this game, and history-wise I think submarine skippers were under-credited. I'm surprised the Japanese didn't respect/fear them more- they could strike anywhere in the pacific, and the Japanese didn't have degree of naval intelligence the Allies did to hunt them down and kill them.
I like your explanation on why different nations did/didn't do certain things. I suppose if the Germany's rigidity is what hurt its submarine force, Japan's doomed hers.
Radio silence and working independently definitely makes the submarine an unpredictable weapon (and since attacking in a submarine is all about having the initiative) but what about the overall sucess of German wolf pack tactics? Were there coordinated submarine attacks in the Pacific?
Finally, just to drive home the effectiveness of American boats, I read that in something like 2-3 separate incidents, an American submarine
sank a Japanese submarine!
Granted it was happening on the surface, but still- I would think in a sub vs sub battle the playing field would be a little more even (maybe they used radar to find the Japanese boat?)