Although this is only part of what I want, I'm going to be focused on what I know well.
First, if U-Boats and fleet boats co-exist in the game, do not share mutually exclusive parameters between the two. Let the American crews speak what they regard as English and let the Germans speak german. Appropriate units of measure for each, let's have strictly segregated code for each type of boat.
Secondly, the plotting system needs to be reworked a bit. Radar positions are just fine, although I would like to see a radar screen good enough to translate a position manually from radar screen to plot and keep the excellent accuracy that radar really had. I think the TMO plotting system should be studied so that players can select no velocity vectors, no friend/neutral/foe colors, no ship silhouettes, no target id, direction of travel or speed on chart. Actually all this should be individually selectable options.
Then there is the problem of what to do with visual sightings. Pretty easy really. There should be a random positioning error of a certain maginitude, growing with distance. That would completely solve the plotting system.
More tools would be nice: bearing rate plots, spread angle calculator or chart, stadimeter plot as from the
Submarine Fire Control Manual. The stadimeter should work as the real one, by setting the real height of the feature you choose to measure on the target. ONI manual should show measurements of multiple masts, funnel height, cabin height, deck height for CVs, etc as the real one did.
In all of this, heavy on the options. The beginner should have his hand held. He should be able to slowly wean himself off the helps in any order he chooses to learn manual targeting by bits and pieces.
I would love to select whether to run on batteries or diesels on the surface, with four diesels and four electric motors/generators independently selected.
The rest of this stuff, others are more qualified than I am to talk about those.