How about the nav buoy making your crews more confident to use their engines at a higher level of power because they have more information about the surrounding area. the sensor arrays could make your guns more accurate by increasing the accuracy of the targeting information of enemy ships. The crews in the bowels of your ship aren't going to be able to see if your flagship is next to them or a hundred thousand miles away. The people in the command deck might be able to see, but they're not going to increase the efficiency of thousands of people, unless they yell it over the radio I guess. My only issue with it is what happens when your controlling a frigate? Will that give the same effect as a capital class ship? What happens if you have two of the same capital ship but one is your flagship and the other one is just another ship in your fleet, does only your flagship give a bonus? Hopefully your finding this constructive, because you do raise good points, and I totally undestand how cool it would be to join a fight in your flagship and change the tide of battle, just trying to make it make sense in my mind.
Mago