Substandard torpedoes for a large portion of the war, treacherous shallow waters, being forced to patrol into the heavily patrolled and mined home waters of Imperial Japan (to put that in SH3 terms, imagine you've just been ordered to patrol the English Channel) and a fanatical enemy with the most powerful navy in the world at the time.
Sure, sounds like a cakewalk.
I wouldn't worry too much about the challenge aspect. Remember that SH1 was a PTO based sub sim and is considered by many to be the best of all time.