I have some ideas:
If you do make alliances, whenever a country in an alliance attacks another country or gets attacked by another country, the country or countries in the alliance will help.
Have a list of every country, old country or even province, and if you click on a country on that list, the country spawns in.
Related to the previous idea, when a country spawns in, you can choose if that country has all of it's land or not. Same with other countries that you don't spawn in with the list.
You should be able to choose what colour a country is.
Sort of related to the list of every country idea, you should be able to have a setting where you choose if that country can get unclaimed land or not.
There should be a setting where you can make force countries to NOT attack at all until you click the attack button and unforce it.
On Custom Maps, you could choose an existing map template and work off of that.
New Caucasus Map.
New other continent maps.
Be able to change the chances of a rebellion/revolt. (per country)
Choose the number of rebellions/revolts that can happen at once. (per country)
Forcing a country to have NO rebellions/revolts.
Option to pick what country will win.
Instead of just custom colours, what about custom flags?
Be able to choose exactly what year a rebellion can happen as long as there is a city.
Force Peace button.
After a country is destroyed, you can click on the country that destroyed it and click on the destroyed country. Well maybe there could be an option to bring the nation back.
Related to the previous idea, you could also pick how much land the country will have when it comes back.
Related to the customizable country colour idea, you could make an option to make the country multicoloured.
Related to the previous idea, you could also pick what pattern the colours are in.
Edit: New idea! The ability to change a country's capital. But just so that it's fair, it has a 2 minute cooldown.