Some ideas I like:
-Modding capability (I know everyone is talking about this, i've read every reply so I can tell how annoying it can be, but it'd be really cool)
-Selective independence (At the start of the game you could have a list to choose which countries are independent and not)
-Formables (When certain countries get a certain percent of certain provinces, they can change their name to a different one, like Italy forming the Roman Empire)
-Deformables (Like formables, but all countries inside a formable become independent.)
-Larger = Harder to annex (Make it so the larger a country is the harder it is to annex by one single country)
-Mouse dragging (Let the camera be moved by the mouse)
-Change "Ivory Coast" and "East Timor" to "Cote 'd Ivoire" and "Timor-Leste" respectively (don't actually know if you've already done this, but these are the official names of the countries)