Yeah, it is very well done, I just think there might be issues if two players claim control over the same units or fight over which units they control using the Native system. I was thinking that maybe using classes would work well by having your class choice designate who you command. For example, if you choose the class "Commander", you lead all the troops. If you choose "Commander" but there's a cavalry captain, you command all but cavalry. If you choose cavalry captain and there is no commander, then the rest of the troops behave with default AI and your cavalry obeys you. Each group leader would also have attributes/equipment options for their troops as well as themselves. Example: Archer group leader can outfit his archers. He can also equip himself, but his stats and capabilities are similar to those of his archers.
Using this system, you could have up to somewhere between 4 and 8 leaders on each side, each with his own role. You would then have to cooperate in order to use effective strategy and win.