
The solution to all this, it seems to me, is to allow the player top level control of all of his ships without them being in the player's squad. Any ships assigned to a top level ship, call it the 'flagship' of that fleet, would no longer be under direct player control, until removed from that fleet. The AI fleet commander would then direct it's ships in a suitable fashion to carry out the player's general orders.
We essentially have most of this already. We just don't have the ability to command those top level ships without putting them in our squad. I think with this rather simple change (partially done already for trading ships) we'd solve most of the current issues with ship control. We could have as few or as many fleets as we wish, and we'd avoid having the super micromanagement headaches of direct control over every player-owned ship in the game.