Well like i said, the Commander doesn’t need to be plot armored, he could very well die. Depending on which game mode (Iron Man or such) it could either mean the end or a penalty. It doesnt need to be a combat role, and despite the Commander having somewhat better stats than your battle brothers, he could still get isolated and killed easily enough like any other battle brother.
Also taking the Commander out to battle would be totally optional, maybe you are in a battle where EVERYONE needs to get stuck in or maybe you were ambushed and thus you find yourself in the thick of things with your brothers, Also with there being a player character, Duels could more directly concern you. Maybe a guy is accusing your company of something and thus you must subject yourself to a trial by combat in order to clear the name of your brothers and yourself or something along those lines.
However i totally understand your point, if this system is not implemented well, it could take from the importance of other characters, as such it should be implemented in a way in which The Commander is still heavily reliant on the other battle brothers in order to be effective/survive.
Another thing would be that when i thought of this, it should be implemented in the game later on, when the map is bigger and there are more factions, as of now, the whole desperate band of mercenaries is a valid point, but it eventually devolves into a quest to level up your company and buy the best armor for your brothers. Having a Commander could make the game have more depth and immersion, it opens up new quests and ideas, but it needs to be done well. Oh and no Import/Export Commander feature, THAT would totally break things if i just Import a SUPER COMMANDER that can One-Man everything from early to mid game.
Anyways i hope i could clarify somewhat unto my idea and forgive me if i did not, this is my first time ever suggesting ideas for the forums.