I've commented on this numerous times in the past, but here it is again. What I'd like to see is the following:
1) First and foremost, to use any of the below requires you to be present on the bridge continuously; if you leave the bridge, you can still modify waypoints, but can't affect speed and can't manually con the ship. Leaving the bridge results in the CV automatically returing to normal speed and waypoint-following.
2) Direct speed control: three or four standard settings, such as "ahead 1/3", "ahead full", "ahead flank". No "all stop", or backing (reverse), since the only time a warship at sea would come to a full stop would be if they're docking/anchoring, launching boats, or rescuing (none of which are relevant to the game).
3) Direct con: basically allows direct steering of the ship via joystick input.
4) Make smoke: all ships in company with the flagship (which is usually the CV, but could be another vessel in a scenario map) begin generating smoke.
I would NOT give any individual the right to prevent players from upping in a gun, or to prevent Otto from firing, though with regard to the second, an argument could be made for allowing the CV commander to reduce (but not to zero) the engagement envelope of the puffy-ack (perhaps make it an arena option?).
Now, some would argue that several of the options above can make it darn difficult to either take off from or land on the CV, but I'd argue no more so then simply turning the CV using the current waypoint control already does. It will, however, make the CV a harder target to hit, when it's being actively conned. From an offensive standpoint, the main benefit would be during shore bombardment; going to a slower speed setting would make that somewhat easier. The downside is, a slow ship is easier to hit, too, and they don't exactly accellerate like a muscle car. Also, there'd still need to be computer code to override direct inputs, so that you can't beach the CV or come closer than the allowed minimum. Note also, that none of my suggestions here would make it any easier or harder to "hide" the CVBG; all are strictly tactical in nature.