I love all the above ideas, but I especially love the "lightening rod" commander/troop. This would be great in that it adds a whole new dimension of strategy to the game. It would be perfect for MA Ulm, like a commander who has been blessed by the god to take upon himself the magical punishment due others.
I also like troop bonuses. We already have standards for morale. I can also see commanders who increase strength, speed, precision, fatigue.
Possibilites are endless, and awesome. It would be cool if abilities were moddable, unless they already are, in which case I'm just an idiot.
