There is one game that i know of that is really strategic and deep in nature where you control one ship.
Anyone here ever heard of the X series? I have X3:Reunion with the XTM mod and it is definitely the deepest space sim I have. Ok, you don't have real damage control or fear of mutiny, but especially in the capital ships you definitely have to worry about your maneuvering, weapons, drones(if you use them), and fuel(though energy is used for warping between systems, not simply traveling through space).
The real depth of the X series though is in its trading and empire management. It's the only Space sim I know where the player flies his own ship but can buy space stations and other ships to form fleets if he wants too. The trading is also really deep with a dynamic economy.