That is a pretty interesting idea. A campaign from the point of view of the bottom up, rather than the top down. A strictly combat game where you start as a single ship commander and move up to fleet commands of increasing size. You might be able to design the ships you use for each mission within certain tech and money constraints. No empire building or diplomacy, just design the ship and go beat down aliens with it. Real time may not work, but "full" turn based tactical combat would be the main focus of the game. It's obviously not something to include in GC3, but as a standalone parallel game it's an interesting concept.
If you're just ship commander, then design is outside of your control, you won't have enough responsibilities to do so. Your job is to command, and to adapt your actions and crew to existing circumstances. Command could give you new ship to test it (whole upgrades system was one of few comlains I had to Nexus, for me it's just outside of our area of responsibility), but that's all. Should we have good records, we could ask transfer on better ship, or request certain upgrades but nothing more.
As I see learning curve of this game it should start in academy - big, mostly text-based tutorial. During it, or after exams, player will be send to different ships, where he would assume different positions. Starting one could be engineering officers, to check player's understanding of maneuvers, and proper use of it. Then we could be transfered to comms/radar officer, where game would tech player to control battlefield, and command other ships. Not necessary through submenues, but it works fine in simulators, so maybe through them. Our next post should be either artillery and/or mines/torpedoes officer, where we show how we understand fighting principles. Final, and most important test is navigation officer, where we serve as navigator. Should we pass this test, we'll be given command of our first ship, some small patrol cutter. Then we slowly climb up the ranks, getting bigger ships, or, if we wish, getting smaller ships units command - say destroyers flotilla.
Overall, game should look similar to Silent Hunter (3, if that's important), but less on simulation side, and more or tactical/control side. So when you'll be commanding your ship, you won't have to control each of the aspects - because you'll have subordinate officers who will do that for you, but should you desire to use some illumination shot instead of sabot, you could order to do that, and your artillery officer should follow your order. But you don't have to control each and every turret (or any other form of armament).
The learning curve I suggested is indeed resemble that of Wermacht officers, where candidates went through all subordinate steps, to sieve only worthy ones, thus guaranteeing quality of officers' corps.