how about at level 100 or so (or make the level vary by perk, and to get the perk you can class the BO to get it), you can give the BO a perk. Make it a one-time-only perk, make it unchangeable (Don't sell a premium item to change it, either, make it 100% final). Some examples:
-"Experienced Lookouts" where you are notified when the enemy can see you. If your ship cannot see a submerged submarine, and the enemy team can only see you because a submarine is providing vision, then you are not notified, and if you are only a shadow on the horizon, you are not notified either.
-"Veteran Helmsman" where your ship's turning force is increased
-"Experienced Spotters" where if you can see enemy shells incoming, you can see where they will land in advance. If the ship's speed is fast enough then this can be adjusted by the devs to decrease the warning time so that all ships will recieve equal chance to dodge the shell, discounting the player's skill and reaction time.
-"A Solid Team" - This perk does not come into effect until level 110 or 115, the caps for your crew serving under that BO increases a bit, but not too much, and SD is still capped at 900.
Although I cringe to think of what the actual implementation of this would look like.