I haven't played FE at all yet (obviously) and perhaps in its current incarnation this already works well or is addressed. but...
"Monsters" in EWOM were semi-intelligent in that lots were dumb but then some could "recruit" them and band up and then attack assets that they would otherwise be too weak to attack on their own.
I would assume that these "intelligent" or "leader-esque" monsters may or may not have originally been involved with more legit occupations under the employ of a kingdom/empire.
So my idea is, basically, that in-game events can trigger kingdom/empire assets to become intelligent monsters. For example, a champion defeated in combat may become disenfranchised with the status quo and become a monster that recruits other monsters.
Also, when a sovereign becomes homeless (all cities are conquered/destroyed) he/she could have the option of recruiting monsters and follow some alternate path to victory (or could choose to remain 'legit' and attempt to re-capture assets and re-build the kingdom/empire).
Also, "monster diplomacy" might be an interesting tech tree branch - hiring bandits as mercs, convincing monsters to stay out of your hair, or eventually recruiting monsters, etc.
cheers,
-tid242