I think it would be interesting if independant provinces could regulate themselves - for example, applying their income to raising defense or purchasing units. So if you assassinated all the commanders in an indy province, then it would buy new commanders or have local defense commanders, so they would not auto-rout. And if you attack an indy and kill half their troops, you need to follow up quickly, because eventually their troops will be replaced.
Ultimately, I think it would be interesting if a strong indy attacked a neighboring nation that neglected its defense. Not invariably, but there should be a small risk of it... it's not realistic to leave a 200-strong knight-and-longbow province in the middle of your empire, and never fear it. Historically, empires have fallen from neglecting their barbarian neighbors...
-Cherry