I'm not sure how to explain my idea, so bear with me.
I think it would be better if you could give more direct orders if you have a small fleet, consisting of frigates and destroyers, nothing bigger. In this case you're not fleet admiral, just a captain/commander of the leading warship, so you could communicate mid battle with other captains of other similar-class warships like it probably happens in real life. Now, when you get a bigger ship, your rank (this could probably either be made into player levels or just a simple ships-class = rank system) would be higher than a captain. For the sake of clear distinction, let's take a capital class ship and Admiral as rank. Now, since you're not a captain anymore, you don't communicate that much with individual captains, you're doing more tactics than battle (Obviously you still battle other ships, but it's more of a 1vsX rather than 2v2, 3v3 teamwork battle). All orders would be like now, kinda widespread and less specific, and it would all come down to captains of small ships to try and figure out the best way to complete this assignment.
I would probably advise against command points, since you won't need lots of them with this system, because its just a few general orders. What I would instead offer is to use command points on direct orders, like if an Admiral sees some rare opportunity that would help immensely or he has some specific plan/tactic that he would like to execute, he could override captains orders/authority and give direct order to specific frigate/fighter wing/whatever. This would fit nicely with limited command points, since Admiral shouldn't give direct orders often or to everyone, but if he has a request, it should be done, because well, he's an Admiral and he's more experienced so he should know better.
As you see, this would leave the current system intact for fleet wide battles, but will give more control for small fleets, if you can call them a fleet. This way it would divert focus for big battles from tactical screen to actual battle, but for people with small fleet/number of ships, they could spend a bit more time on tactical screen because it would be less frantic and hence consume less focus but give same amount of control in a way.
Thoughts?