Anothing interesting suggestion I have been pondering, though the chances of Paradox even seeing this are minute:
Allow the player to negotiate with rebels (the red-black ones, not civil war opponents. Edit: though it would be nice to be able to negotiate with civil war enemies - see Mark Antony vs Octavian before they became political allies) in much the same way as barbarians. Be able to demand a surrender if a rebel army was surrounded by your own armies. Be able to create vassals if the rebel army takes a province. Be able to offer a tax reduction if the rebels disband, and so on and so forth. Not all armed revolts ended with all of the perpetrators being slaughtered, despite what Crassus would have us believe.
On the topic of barbarians, I like how 1.3 made barbarians more likely to assault towns. However, whenever a province is taken, they move onto the next province, allowing a careful player to re-capture any lost towns while the barbarians are busy besieging another. Maybe it would be better if barbarians would stop trying to conquer after taking 2-3 provinces (depending on the size of the barbarian army), allowing them to better defend their new lands?
Most of all, and I've already raised this point earlier, would be to have pop-up windows (ie events etc) appear somewhere other than the centre of the screen. All of the player's attention is usually fixed on the centre, as this is where the action is, and it irritates me to no end to have several events pop up during the middle of an intense war. It's easy enough to hit the pause button if this happens, but it's still frustrating.
Anyway, just some little things if the Paradox fellas decide to have a look.