Speaking of thousands of ships - isn't that's why we have chain of command? Division commander does not excersize direct command over each of 10000 troops in his division, probably he doesn't even know all of them, and even all officers. He commands his division as a whole, he has his own "chief of staff", who designs attack plans and keep close communication with supporting units commanders, to know how much fuel, spare parts, ammunition, food, water, medicine, clothing, tools, armament, any other required supply they have. Also he (chief of staff) communicates with different form of reconnaissance units - be that engineers, radio/tech, air, NBC, meteo - simply to know where they could go. You can compare commander with composer, while chief of staff with conductor, if you want. Anyway, there are several regiments in division, and divisional commander and chief of staff will communicate with them. Regimental commanders in turn with lead their regiments, and will communicate with battalions' commanders, who, in turn, will communicate with companies commanders.
So in each moment each commander had to communicate with 3-5 people, that's usually within human hardware throughput, when it comes to processing information. In terms of gameplay, this could look like Hears of Iron, or, if you like. Sid Meier's Gettysburg - we had units of various size, but we had no control over individual soldiers or tanks.
Do I want to see that kind of combat control in GC? No, I'd prefer to have no combat at all - there is military chief, it's his job. All you had to do is tell him how you want to prepare your army, and he'll tell you what budget you need to allocate. Should you plan invasion - again, he'll give you details and you pick those you want to be completed - thorough reconnoissanse, or brief one, induct blockade and long siege, or swift, massive attack, or partisan actions. Not even sure you need to give him advices how to attack - I'd say that should be his job, to act accordingly to existing armed forces and budget.
In the same time, I don't mind GC "spin-offs", dedicated to lower level of command, where we could don admiral's hat and command our glorious fleet from our flagship "pwner". Even lower level of command-game, natural tactical level, Nexus scale, or, I don't know, Blitzkrieg - something within captain/company level of responsibility would be nice, maximum up to colonel/regimental levels. But not in GC. That's the game of different scale - it's galactic civilizations, not borough civilizations.