From a command point of view, there are a couple of things that can make things particularly tricky.
In the past, I have found that if I were to set a course that deliberately took us past and enemy fleet, it would end up ‘bending’ around to engage the enemies head on. The helms officer would have assumed it was an oversight on my part and the course must have been off by a few degrees. In actual fact, the aim would have been to take the ship past the fleet and attack from a specific direction, for example attacking from the opposite side of a base to draw enemies away, or bypassing other nearby enemies to attack a different target. I have had to abandon many plans due to such instances. Sometimes, in the heat of the moment with everything going on, it just isn’t possible to outline clearly or in detail exactly what is being planned by the captain.
From a fleet perspective too, there are very few captains willing to sacrifice a base. There has been more than once that a ship has made a sudden move to defend a base, putting it out of position and causing me to plan around it, rather than come up with a more effective coordinated defense. Again, it might be because they assume I have made an oversight (which is a fair assumption to make), but most of the time I find that I am part way through formulating a strategy (even sending orders out) when ships have jumped into action without clear direction and forced me to re-think (or cancel the orders).
It can be incredibly frustrating. I know the silence over comms can be difficult when it is clear that the enemy is closing and we need to engage, but I think we sometimes forget that others might be receivig orders. The one way around could be to broadcast orders to all at the same time (which on occasion I have done) but this can possibly interfere with bridge comms and so is not a preferred method.
I do think the ideas you have Nhaima are good. When there are two many ships to handle, drawing them off and delaying them from attacking a base is key. What Verok added is equally relevant too. Consider what happens if too many bases are under attack. If two kr three ships are tied up defending multiple bases, whilst another is trying to combat incoming heavy fleets, it can be too overwhelming. Effectively, our force is spread too thin and the need to fall back to create fewer stronger positions may arise. A quick response to a fall back action is important in that instance.