-Realistic navigation option: no more GPS-accurate locations of your submarine given on the map. The accuracy of your position will depend on the weather, time of day, visibilty, and the experience of your navigator.
-Limited rations: we already have limited fuel, so why not limited rations? Each boat carries a set amount of rations (say, 60 days). Each crewmember consumers one ration unit per day, and if he dies, then his remaining units go into the overall "ration pool." If food runs low, you can cut back on rations, but this will have an effect on the crews efficiency and morale.
-Realistic torpedo loading: if the sub tilts more than X number of degrees, the crew will stop trying to reload torpedoes. WWII era subs needed to be as level as possible for the crew to be able to load the tubes safely and quickly.
-More coastal traffic for the Japanese.
-Realistic numbers of capital ships. Sink two Yamatos, and that's it. They won't magically reappear at a later date.
-Proper voice comms for the crew - things like saying "Double oh" instead of "zero zero", and (
) "rudder amidships."