Okay, here's a list of stuff I'd like to see:
First-person perspective where you actually walk up the gangplank and get in the sub, also allowing interaction on the land for things like briefings, training and giving awards etc. Walking about in your sub.
More systems modelled so that you actually get realistic ballast and trim problems that you have to figure out solutions to.
Interior graphics that drip water and get messy as time goes on, balancing how much this bother you and whether you choose to order more cleanliness affecting morale would be good.
Interactive crew, with the ability to get them to learn new tactics so they can drive the sub for you on your preferred attack course etc. Especially an XO with more interactive capability, such as tactical suggestions, recommendations for awards from chiefs of various shifts etc.
Crew members that don't fit in (the virtual Bernard if you like).
Crew members actually saying things, I seriously doubt that a gunner who has just shot down a Jap flying boat would not yell 'Take that you Jap b*st*rd!', and you could be damn sure the crew would cheer.
Political concerns, Nazi party members on your U-Boat, Jewish crew members etc etc. Arguments between crew members when they get frustrated by your crappy performance and the ability to decide their punishment (if any), even just a few numbered options would be a start! This is what commanding a submarine is about, not drawing a course line, that's the friggin navigators job!
Risking allowing your crew to sunbathe on deck. fishing off the deck.
The Focke Achgelis Fa 330!
Tidal currents, fish, whales, dolphins, seabirds on the water, oil slicks you can follow on the surface, food dumped on the water by careless convoys so you have to work out tidal flows, or at least ask the navigator to do it!
The light affecting tactics more than it currently does!
A link to real world weather via a download, to make seasonal stuff possible (flight sims have this capability, and have had it for at least 5 years in the mainstream).
The need to service the submarine and maintain its machinery, even via delegation would do, so that you could be caught with your torpedoes not 'ready to rock'. Real WW2 torpedoes did not sit in their tubes for three weeks while you drove about looking for targets! Trim dives, finite food storage. The ability for your crew to innovate and improvise stuff.
Confiscating supplies off merchants you stop, picking up food that floats off sinking ships, taking prisoners on board, interrogating them, giving them supplies and and directions to the nearest landfall.
Crew morale based on all these elements (I know this is sort of in there, but it's pretty basic). Your crew would not think you were great if you machine gunned a lifeboat, then again, maybe they would if you'd picked a bunch of Nazis for your crew or whatever.
Damp conditions and poor weather affecting morale, the cook affecting morale, whether you allow booze on board, or smoking.
Progressive rust and damage to your exterior sub model the longer it stays at sea.
Victory pennants on your conning tower.
One problem why we might not see these however, is that many game/sim companies do not 'lead from the front', instead, assuming that sub sims are a limited market. However, with more foresight, if they made the most ass-kicking, envelope-pushing and innovative sub sim ever, I suspect not just sub sim fans would want to play it. The most succesful companies tend to take this approach, an example being Boeing, which gambled when it built some of its most successful products, including the Flying Fortress and the Boeing 747 Jumbo.
If you build it, they will come, is something computer sim companies should bear in mind.
Chock