It's a great idea, one of the best! If you do so, make sure the RTS can signal the dragon what to do (by placing beacons etc). Maybe a little dragon support (flying minions not controlled by RTS player) can help.
But since the dragon knight would no longer 'command' the armies, it's no longer Dragon Commander isn't it? You're putting one of your generals in charge... unless you got the power to split your mid of course... just figure something out
But yes, you should definitely do this!
