Actually, this gives me a great idea.
Imagine Team Fortress 2 with that commander character. He looks through his available units (Soldier, Heavy, Medic, etc.), and you give them suggestions on where to go and what to kill, what objectives to take, who to stick together with. This makes winning is a matter of teamwork. They don't HAVE to listen to the commander, and very well may win if they don't, but if they're fighting against a team that's well coordinated, then they'll probably have significantly less success, unless they're significantly more skilled.
He would issue commands by clicking on one of his players, right clicking something to say "move to this location" or "Attack this" or "Defend here" etc. You could also set Fireteams, where you want a certain group of players to stick together, maybe a Heavy and a medic, or w/e combination you think is best.
Now, maybe this can just be a secondary mode, like capture the flag or other similar play mode, instead of being the main meat of the game.
And of course, this would be great for clans. The clan leader can recruit people, and they'll be more likely to listen to him because of a bond of friendship.
Maybe it wouldn't work too well for Team Fortress 2, specifically. Maybe it would be better suited to a game like MAG, or perhaps better might be to come up with a brand new game in which you carefully tailor the classes that can be played to fit with particular strategies.
Oh! And we can't forget resource mining. Let's removing the mining aspect, and change the resource to money. Every time one of your blokes gets a kill, you get some money. This can allow you to upgrade their weapons, armor, perks, etc. Maybe you can have some cheap upgrades that give your bloke a better weapon until he dies, and some expensive ones to permanently upgrade it. Much Strategy to be had there. Do you upgrade your weapons right now for cheap to get potentially more gains, or do you save your money to buy the permanent ones that will give you the edge later in the battle?
This could easily break up the monotony you usually get in an online shooter like CoD. Usually, after the first 5 minutes of a game, you already know who is going to win. Sometimes the tides turn, but it's rare. At least, it is in my experience. But, buffing up one side with upgrades because you have a commander who knows his shit? That could very well turn the tide of a match.
Perhaps, if you can't get players to work together, create a rewards system. Every time you complete an objective that your commander gives you, you get a temporary boost to your character. (Besides a move command.) So, say you kill the bloke that your commander had you targeting, perhaps you get your health refilled, or you get a damage bonus, or something of that nature.
Now, maybe this game needs to be based on an open field, with lots of structures placed along to please the people who like to hobble around corridors and such. Now maybe you need to have it so you can build buildings. Fair enough, let's see what we can do about that...
Add back in resource mining. Take the Command and Conquer approach. Build a foundry, have a harvester NPC, make it a tactical advantage to control certain areas that will give you an income. Perhaps have some buildings where if controlled, your team gets particular bonuses, or a big ass turret that shoots at passersby. Then maybe you can make it like Battlefield, you can build tanks for your team to use, or have stolen, with your money. Maybe even fighter jets and such. Perhaps you could have these as minor support upgrades, that only help marginally, but this worked for battlefield, so I don't see why it can't work here. You could even have specialty vehicles, and maybe you could have a character that gets damage bonuses and such for being in one of the vehicles.
Unless you could get a game as big as MAG with these aspects, you would have to keep all these things very small-scale, however.
Wow, this post is huge. I could go on and on past this about some ideas that came to mind, but I think I might break The Escapist if I type anymore.
