Before we get too far into the simulated personality in charge type setup here let me say I had no such intention. I find the setting commanders and governors type gameplay be rather annoying...the user is either in command or not. Furthermore the flow of battle is far too fast to enable meaningful 'personality' behavior modifiers. Setting fleet behaviors does essentially the same thing while not tacking a face to it or forcing you into a particular option set.
Having to set and use avatars and sub commanders in that fashion makes sense in Total War historical type simulation or pure a pure simulation, but is cumbersome unless your going to limit yourself to a semi turn based play style.
In fact most of the limitations in scope mentioned so far in the discussion seem designed specifically to eliminate or substantially diminish such play style.
-However ...although I do not approve of this play for the user I do believe in behavior modifiers for the opposing agents. By adjusting the fudge-factors in the weighted random states of the sub-commanders would create stronger groups of behavior. This would allow stronger campaign setups as the user finds himself going against multiple personality command styles.