I want tactical combat. I don't want control over individual ships.
In RTS games, individual unit control leads to high action counts winning games and ridiculously gimmicky things like running units around in circles while other things kill the ships stuck chasing them.
In TBS games, it just leads to one of two things. A nightmare, or extremely limited scope.
If you had a thousand ships in a fleet, that would be awesome. In MOO, they'd have been in stacks, which is gay but not so much. If not in stacks, a tactical combat between thousands of ships could take hours. Who would want that? The result is silly things like "armies" being 9 units max and other such silliness to get around the management problem of large unit counts.
My own personal dream system would be some sort of squad based real time implementation. Ships would have command cruisers of some sort that were the control unit. Tactics and general directives would be issued. No micro level directives. Defend here, retreat there, patrol this. No attack this ship. With an AI that learns from player behavior, AI could get extremely good at building fleets. With a more realistic command method, they wouldn't have to worry about silly little things like focus firing particular ships first, individually retreating damaged vessels. The nonsense would be largely cut out.
Fleet sizes would then be determined by how many command cruisers you could network, and how many ships those command cruisers could coordinate. Logistics in essence. With no micro level control and fully automated individual ship behavior, your direction would be meaningful, but largely lack in cheapshot methods of accomplishing things.
I say real time only because no matter how streamlined the system is, turn based tactical still ends up taking far more time unless the damage rate is very high. A high damage rate leads to an increasing inability to compensate for clever human behaviors in positioning. I'd prefer simple pre battle settings to turn based tactical combat. Simple design level settings like close for attack, stand off, evade.