Morale is a good idea, games have always bugged me when battles almost always result in the total annihilation of one side. I've been planning on adding it in some capacity in a future update, with Nobles that can boost the morale of nearby troops. Instead of making the Nobles frail, however, I'm thinking they should be strong. The Noble and his guard would be equipped with the best gear money can buy. The Noble could die permanently, however, and would be hard to replace (I really like that Risk/Reward aspect of using generals in Total War).
I'm not sure how to handle logistics. I'm leaning towards an invisible supply line with limited length, encouraging the creating of support outposts which would be easy for the AI to attack.
Player controlled raiders are a good idea, but right now there's nothing for them to steal.