A neat idea (just a fantasy here, bear with me) I had for SHIV is a supply system in your submarine. Since US subs made long patrols, I'd like to see more than just fuel be a limiting factor. Here's how I envision it:
Your boat has a 'maximum displacement'. This is the absolute limit of crap you can fit in your boat. There are three primary catagories of supplies:
1.) Consumables- This consists of food/drink/medicine/coffee/ice cream that your crew needs to eat. All militiaries run on their stomachs, and I wouldn't imagine a sub crew to be any different. Just as you can travel slower to conserve diesel, you could vary rations to conserve consumables. High rations=high morale, low rations=low morale/greater crew fatigue. Maybe random events, like a crewmember falling violently ill or having an accident doing routine work (hey, its a dangerous job) which causes him to be laid up and drains supplies. In base, you can decide how much you want to bring, with the game telling you the estimated duration in days your supplies will last.
2.) Spare parts- Rather than simply have damage either be quickly repairable or utterly non-repairable, have it work in a spectrum. Depth charges rattle a few bunks loose? Fix it in a jiffy! Engine fried? Hmm, I hope we remembered to bring enough spare valves/pistons...Screw shafts bent like a pretzel? Wonder if the current will eventually drift us back to Pearl...
this way, depending on how conservative you are, you could have damage that you may or may not be able to fix. Making the repair times realistic (and maybe a little more random) would also make it exciting.
3.) Special- This would be stuff for special missions; space allocated for downed airmen you rescue or enemy POWs, commandoes, reconnaisance equipment, supplies for other ships, etc.