It would be awsome if one part of a country and another part could have different religions, there could be new cards like a "split religion" card wich would allow you to paint in the religion map and other cards for it, there could also  maybe be langeuges, races and cultures but adding all 3 might be too much. the origin could also be used as race and a sertion part of a nation could have a different origion. in the country info menu on the right, it would show the biggest religion or origion. (sorry for spelling mistakes)

yeah the race mechanic seems like a good subsitute for the origion since it bassicly already is just the culture/civ the current nation descended from. additionally it would be cool to have relgion paint inside of areas controlled by nations. 

Looking at now it might be too much probably to have things like languages and splitting religions.. Though you could just make "small splits" count as having a vassal from the original nation so that it seems as if they are just a province of the whole nation. By that you can also change "provincial" and "area" religions