I may be going against the grain here but I'm all for the manual controls. I don't mean to sell what the devs are doing short but, this game isn't Sub Command / Dangerous waters and it isn't part of the silent hunter series. DW you basically put the ship on auto-pilot while you did your thing in the realistic sonar and TMA plotter (which if you knew what you were doing you could do better than the computer), for silent hunter, aside from the stunning visuals (which truly cold waters has matched and surpassed lo these 10+ years later) you had the whole crew simulation and 3d stations and walking through the boat.
Cold Waters doesn't have all of that stuff to do if you put the boat on auto-pilot, but I feel that it's disingenuous to what the game is to expect that from the devs. "Gee, this game isn't Dangerous Waters, but if you could make it more like that, that'd be great."
Now for my list of demands
1. In Campaign mode, maybe think about introducing some more generic objectives. I may be going a bit too old-school here, but recently I've digested "Silent Victory" and the "Hitler's U-boat war" books by Clay Blair Jr. and I have a few observations. Obviously things have changed since WW2, but for the most part the majority of the patrols that US Submarines were sent on were fairly straightforward in nature. "Go here, sink what you find, report in and head back when you're out of fish." (Obviously I can admit the war in the Pacific mainly targeting Japan's poorly escorted and regulated merchant fleet is a little different than taking on the Soviet Navy in the Barents Sea) I feel CW is missing a bit of this, the mission objectives are always very specific tasks to accomplish and always have specific outcomes (pass/fail). While this is very effective at moving the campaign / story / picture along it does lead to making you feel that you've got the world on your shoulders.
I guess what I'm getting at is, much like the Silent Hunter games, missions tied to particular geographic locations, or probably more sensibly a "patrol box" area. In some ways the campaign already makes us do this now "Go to the Denmark Strait to prevent an Oscar II from breaking out into the North Atlantic" but what I'm proposing is "Take up station in the Denmark Strait and maintain barrier patrol between Iceland and Greenland", in this case maybe the Oscar comes through, maybe you get an ELF message tasking you with going after the Oscar, or maybe nothing happens at all and you get a new tasking later.
Another opportunity here would be maybe for "reconnaissance / stealth missions" (also I have to apologize, the vast majority of my game-play is in the 1968 campaign so I most likely am overlooking stuff that you guys have in the 84 campaign). While I think going back to a "peace time / Blind Man's Bluff) may not exactly be suited to the game / AI, it may be an interesting challenge to come up with something covert where you're objective it just to listen and classify what's there, then try to escape unnoticed vs. going full on bull in a china shop and tearing the whole place up. This could range from say a mission tasking you to figure out what ships are leaving Murmansk, or maybe a different one where you have to try to locate the "main body" of a Soviet Fleet centered around Kirov or Kiev and then reporting in so that it can be attacked / countered by something greater than just a single submarine.
2. Work on changing the "frequency" for some platforms. At this rate in my 68 campaign, I've sunk so many Novembers that they've got to be pumping some of them out and scraping the barnacles off because they just can't be building new ones this fast. Conversely I can count on one hand the number of times I've seen a Foxtrot class, even the mighty Victor is more common. Can understand a bit with the Romeos because they had very low production numbers and the Whiskey is pretty abundant too.
3. Major pie in the sky and maybe a little bit too far reaching. Rather than considering getting into a full blown crew simulation as a few have mentioned maybe a series of optional (as in you can turn this off if its not your cup of tea) random buffs / debuffs to blur some lines. I'm meaning stuff like
"Overdue for refit: If things were different, your boat would be high and dry getting her bottom scraped and repainted. As it is, wartime considerations have meant postponing your refit and now you lose 5-10% of your top speed due to drag caused by marine growth."
"Brand New boat / Fresh out of dry dock: Your boat now meets and exceeds all design specifications for her class. Enjoy top speed and maybe even a little more!"
You could do the same with some of the departments, like Weapons / Engineering / Sonar for faster/ slower reload / repair times and shorter / longer detection ranges or more / less accurate TMA (all within a reasonable few % range up or down). What I would suggest though, rather than having negatives (Your Weps det. sucks) have unknowns (Rookie weps det.) which may be anything in the range of bad to good. Lastly, make all this assigned randomly so rather than leveling up / upgrading certain areas / unlocking abilities, much like I assume goes on in the real Navy, you have to work with the equipment and personnel you're given and no two boats are exactly alike. This would make the game a bit more fuzzy (instead of knowing for sure "I can do X thing because I'm in a Skipjack class!" you're wondering "Can MY Skipjack class sub do X thing?"