Originally In Nomine was supposed to be the last expansion pack released for Europa Universalis III but the developers felt they had more idea's to add to the game. There won't be an extension to the time line and instead there will be a complete focus on game mechanics, historical flavour and more balance.
A Dynasty system has been added which ads more depth to monarchs within game and ads more to abilities such as Royal Marriages and Personal Unions, now an heir is selected and they are given a rating from weak to strong on how strong their claim is and whether or not there is a potential for a succession war occurring when they rise to the throne. Legitimacy has also been added to the current Ruler. If a ruler has a legitimate claim to power and everything isn't going wrong they find themselves with bonuses to their stability. However if it is low they will find there could be problems for them on the horizon. When your current ruler dies and the heir is in his infancy a regency council will still take control, if the legitimacy of the heir is particularly low the regent may try to depose the current dynasty!
There will also be more depth added to the Holy Roman Empire (HRE), first off Imperial Authority, The more the Emperor has the more power he has over the other members of the HRE. This leads to a separate chain of events and decisions which could ultimately end up in the union of the HRE under one banner. The Emperor has methods of raising relations with other nations as well instead of using gold. Members also have the ability to demand other nations to convert to their religion, if rejected they gain a special casus beli they can use to declare war without the emperor interfering. As time goes on the abilities will change as well.
Permanent Terra Incognita will be removed which will make a larger game map, some of these area's as technology evolves will be able to be colonized later on in the game. Such as parts of Northern Russia and Scandinavia, other likely locations include parts of Canada and US. The world map in places such as France and Germany is also being altered slightly for balance, some provinces going to other nations in order to tone down Frances initial starting power which in the past lead to them dominating Europe.
Magistrates have been added, they are gained slowly at first but as a player works their way up the government ranks such as Absolute Monarchy to Constitutional Monarchy they are gained at a faster rate. Magistrates allow decisions to be made, the more you have the and the faster they are gained the faster they can be implemented.
Sphere's of Influence will be added in order to give the greater nations more AI and goals, England for example could spread a sphere of influence over Scotland meaning any aggressive action taken by or against Scotland will mean England can interfere on either side to their advantage. This is also to encourage more wars between the greater powers interfering with each other's sphere of influences.
Casus Beli's will be expanded upon offering more choices for war, this also restricts being able to take everything at the negotiating table at the end of the war as each one is catered towards reconquest, religion, succession ect and therefore what you can get out of the war at the end is different each time. This also affects the title of the war. Rather than "1st English War of aggression" and then rising with each war. They now gain there own titles such as "English reconquest of Normandy" adding more of an historical flavour.
Merchant Republics are receiving an overhaul. Based on the Hanseatic League, a nation which now becomes one in itself. They gain the ability to set up there own trade leagues, members within don't compete with each other and have the chance to gain bonuses to their trade. This gives the Merchant Republic the chance to control trade more to their favour and profit from it more. They will also now have a new set of events and decisions which affect them in different ways.