Once upon a time there was an age in which subsims were popular. Partly it was due to novels such as Tom Clancy's "The Hunt for Red October," but also because of Cold War fears which permeated the culture of that era. After all, just one "boomer" carries enough nuclear warhead tipped ballistic missiles to devastate an entire continent. Couple this with the fact that such an underwater vessel can keep its whereabouts a secret for months at a time, and you have what is essentially the ultimate weapon of the modern age.
However as the years rolled on and the Soviet Union came to an end, subsims shifted away from their high tech forms back to historic conflicts of their heyday. Basically, you can choose between Americans in the Pacific or Germans in the Atlantic but regardless it's always World War 2. There's nothing inherently wrong with being stuck with U-boats instead of SSNs except that there's a lot more that a modern military submarine can do. For one they are capable of engaging targets on land, sea or in the air (not to mention other underwater craft). Technology also allows for a much greater variety of missions and tactics.
The whole concept of undersea warfare is a game of cat-and-mouse. Sound is vital to situation awareness since very little light penetrates to the depths that most submarines operate at. Don't forget that beneath the waves it's a fully three dimensional environment complete with trenches, seamounts, ridges, troughs, plateaus, reefs, atolls, sea vents and sunken ruins (not to mention deep rivers and lakes). Couple all this underwater topography with background noise generated by eddies/currents and there is a lot of places to hide.
On board passive listening devices only work when moving slowly. Worse yet it can be difficult to properly identify, let alone hear, other vessels. Active systems such as sonar can give a clearer picture, but even they can be fooled by staying near the surface or close to the ocean floor. The reason for this has to do with the sound reflection lacking detail if the ping has to travel far. Pinging also has the disadvantage of revealing one's position. Of course it is possible to channel sonar only in a certain direction. Depending on the frequency the range can also be limited to a degree. Lashing foes with loud pings can be a viable tactic since the noise generated will blind and confuse listening devices.
instance of a submarine sinking another while both were submerged. Despite this all modern subs have a cache of torpedoes. Unlike the original straight running "fish" used in the past, current versions use guidance systems to zero in on their targets. However, even this advancement in navel warfare hardly guarantees a kill. Acoustic tracking can be fooled by noisemakers. Magnetic guidance systems designed to turn toward ship hulls are tougher to foil, but even these devices are vulnerable to countermeasures. Obviously manually steering the torpedo by wire might seem like the best option, but this too can be tricked by signal scrambling pings from the target. Remember that submarines carry a very limited supply of ammo, and as such cannot use it's weaponry indiscriminately without quickly running dry. Reloading takes a fair amount time too which is the reason why most combat subs are equipped with four or more tubes to fire from. More than once a submarine has been destroyed by its own torpedo coming back around. Fail safe systems can, and do exist, but these introduce problems of their own such as minimal firing distances.
In combat situations underwater blasts cause a kind of blindness in the form of dense clusters of bubbles which disrupt sonar and mask other sounds. Obviously these pockets rise slowly to the surface, but the fact remains that explosions from depth charges, torpedoes, mines and so on, create their own form of exploitable phenomenon.
Ken Levine (maker of Bioshock: Infinite) originally started off at the now defunct Looking Glass Studios writing design docs for stealth fighter and submarine games. Eventually his ideas were used to make Thief: The Dark Project, and while I love that series part of me wonder what a story driven subsim would be like. Setting it a fictional oceanic setting like the Ace Combat franchise would allow for a lot of freedom when it comes to scenario design.