So, thinking back over all the games I've seen that employed a squad mechanic of some sort where the characters are relevant, command has never been a viable role. Squads are always full of specialities: snipers, engineers, hackers, heavy gunners, rocketeers, pilots, a plethora of specializations. Sometimes a stock soldier exists, but there's rarely any point to play as them. And what's worse, even with the auspices of military organization in a huge number of games, rarely do they actually implement command as a gameplay mechanic. Either objectives are assigned and progress is prohibited if order aren't followed, or orders given are totally pointless and you're free to do whatever you want.
The idea I was tossing about was to introduce a command role, and give it a real point. Just for a bit of context, the setting involved essentially a 3 man mercenary squad, in which I wanted to emphasize each character being a proper character, not an extra gun for you to boss around. So we give the player a choice between these three people, who fall into a few tropes. A sniper, an engineer and a leader. The idea was that each character had their sphere of action, and the leader, instead of a big gun or a mortar strike or anything like that, would get freedom. The commander is free to choose how to approach objectives, which objectives to approach in the first place and when he issues commands to his subordinates, they will be followed.
However, the part I haven't seen implemented before was what might happen if you chose to be the sniper or engineer. They don't get freedom. Objectives are selected by the leader and they're ordered to positions and commanded to perform actions, which the player will have to carry out. The player is of course free to to ignore those commands, if they think there's a better way to do it. But breaking rank would have consequences in a soft karma system. If you run off and choose a sniping roost the leader didn't point you to, there'd be higher chance to get flanked and attacked from behind because you're not somewhere your mates can cover. Or consequently, you might be in the wrong place to cover your mates and they can get injured/killed because you prioritized killing enemies over protecting your mates. Following orders would get greater help from your mates like calling out targets better, or pointing you towards a loot cache they noticed. Even such responses as making the enemies smarter: Thugs often might not know how to tell where a sniper shot came from and duck inefficiently, but a renegade sniper would find his targets hiding better, or being more alert.
Just food for thought, trying to spread some ideas I've been tossing around, feel free to discuss and/or implement.