Everybody has great suggestions, but have patience. All these things will come with time. In the meantime, we should enjoy what we have, which is darned great!
I don't see any problems with all the details, so long as there is a heirarchy of options to let you phase in the use of real navigation, engine options, ballast tank management, fuel tank management, sonars individually accessable and useable (there were at least 3 on American subs), radar realism, radio coding and decoding, MoBo or something very like it should be incorporated into the game for realistic plotting.
But these need to be options that don't lock the casual player out of the game. If you don't have fun from the first startup of the game, it will sit on the shelf. Realism doesn't have to be at the expense of playability.
And finally, actual schools where you learn all this stuff in the game with an instructor in real life training situations.
Folks, you're looking a minimum of five years before anything like this is possible. You're looking at ten years before it gets installed on a single user computer. It will foster a whole new generation of complainers just as bad as this one.