Could take a leaf from Airships: Conquer the Skies, and give every ship an Order Delay.
You can give an order or group of similar orders almost immediately (as long as, of course, you haven't given one recently, since that would mean your flagship's comm equipment and crew is busy - skills and hullmods would reduce that a lot. My view on Similar is you can issue the same command on multiple targets, or the same command TO multiple targets, but not different commands. "Avoid this this and this", or "Escort this one and that one, with those ships on this escort and those other ships on that one" but not "Avoid there, strike there, and you, escort that")
A ship can receive an order almost immediately, but then can't receive a second order until its Order Delay has passed. CR percentage or Officer stats/skills would probably be the biggest determinant here, though I'm sure there could be some other modifiers.
This cuts out much of the "I told them to do this, why isn't it happening!" player confusion, but maintains the "You have asked too much in too little time".
Since you can then display this order delay on the tacmap (both your own, probably via the top-right timeout bar, and other ships, maybe some sort of ring around them than fills in or something), it is also a lot more discoverable than any queuing system. One might argue that a queue would make things easier to manage a large number of different commands, but that almost seems like it's going against the change you're proposing.
It's an interesting idea. I'm not sure I'd -like- the idea, but I'd certainly like to -try- it!