An idea.

[BobRoss0902]

What I would love to see is a system similar to what Graviteam Tactics Mius Front has, where you cannot order your soldiers unless that squad has an alive squad commander, or you have moved a commander nearby them.

Basically this means that a bridge hit could mean that unless the ship is within visual/radio range of your flagship it gets taken over by the AI and does what it thinks is best.

You could also train crews to be "squadron commanders" where let's say a squad is away from the flagship, then the ship in front of the squad commander gets hit on the bridge/conning tower. You can still order both of them since there is a squad commander nearby in visual/radio range.

[Danvanthevacuumman]

interesting yeah

[Cpt.Hissy]

More or less how it works in Rule the waves on less easy setting.
Everything that has no visual contact with your flagship isn't controllable. More so, they don't magically sense enemies if flagship sees them, they don't also know where flagship is and may wander off in completely wrong direction and pop out of the battle. Same with enemies.