Europa Universalis III: In Nomine

Europa Universalis 3 : In Nomine was released worldwide through Paradox Interactives Digitial Distribution service Gamersgate. It was what the Paradox Devs described as the "final coat of polish" the game needed and overhauled many of the games features. It expanded the timeline back to 1399 adding 54 years to the gameplay.

Religion

Religion got a massive overhaul. The tolerance sliders were removed and your countries tolerance religion is now affected by National Idea's and Religious Decisions.  Missionaries our now much cheaper, but they do require a monthly upkeep. Missionaries stay untill the target province is converted or untill  they are cancelled. The Papal Controllor also got new abilities, they can now Call for a Crusade which gives bonuses to nations that declare war on the target.  Catholic nations can now Excommunicate other Catholic nations.  Catholic nations can declare war on excommunicated nations without suffering the usual stability hit. And finally there is no longer a stability hit for declaring war on a nation of another religion.

Missions

The Mission system now gives missions to every nation on the map, they can be historical such as the English need to conquer Ireland, or they can be generic missions such as England need to build a University in London. Not every nation has historical missions and instead are regularly given generic missions. You get a reward for completing a mission, In Englands conquering of Ireland they recieve a core on every province if they succeed.    
                                                                                                                                                                    

Decisions

The decisions system allows you to have more control over your nation, there are 3 differend kinds of decisions available. National decisions are normally historical in Englands case if they manage to unify the British Isle's they can become Great Britain which gives them bonuses, this replaces the potentially long wait to become Great Britain. 
There are also Religious Decisions trough these decisions  can change  your country's state religion. And finally there is the provincal decision which allows decisions to made in individual provinces for example  A sea based province with a Naval Manufactury can speed up its construction of a Navy.
 
 
 

Rebels

Rebels also had an overhaul, they can now get there own leaders such as Oliver Cromwell during the English Civil War. There are now five different types of Rebels: Peasants, Revolutionary, Nationalists, Pretenders to the throne and religious rebels. Rebels have also been made stronger. 

Colonial/Economic

Colonial management  got changed , the growth of the colonies is now affected by colonial maintenance which requires a monthly payment. Instead of Taxes, Tariffs were introduced for the colonies. tariffs are determined by base tax value and the size of your navy. Trade goods are now unknown until they are discovered, and that is then determined by an event. Overall it became much harder to maintain and even keep your colonies as they really hit the monthly income.

Trade goods themselves were reworked and there value in a Centre of Trade were changed and can now be affected by being at war. Inland Centre of Trades are now less valueable than Coastal Centre of Trades. 

Changes to the Warfare System

Warfare was also overhauled, War Exhaustion has become harder for a country to deal with, which increases the chance of rebels appearing as result of a long war. War exhaustion is also influenced by winning or losing battles and wars. Mercenaries no longer get reinforcements and require an higher upkeep. they can now be built in captured land. Armies can no longer retreat within 5 days of battle, if an army faces a force double there size and their moral collapses the army collapses. It is shown in peace deals whether or not the AI would accept (asked for by many fans). Capitals can be demanded in a peace deal.

Navies were also altered, their national idea's were improved, they can be ordered to patrol. Pirates are now much more common and can have leaders this is another factor in making colonal maintence higher.

Changes for the Holy Roman Empire

The Emperor can now declare war on anyone  who declares war on a member of the Holy Roman Empire, but if the emperor chooses not to defend a country from the Holy Roman Empire his relationship with the other members of the empire will suffer. It's now also possible for countries to leave and join the empire with the Province Decision ability, making it much easier for a player to decide whether or not to get involved in the empire. Human Electors can now vote who they want as the new emperor.
  
 
 

Map Changes

The map was changed, 33 new provinces were added, most of them in Europe. The map textures were improved. 2 new map views were added: Cultural and Regional. And the colors were greatly improved to give the maps a better view.

Other Changes

Lastly there were many small changes, the AI itself was given a major overhaul to provide a much better challenge. All the national idea's were modified 10 of them now getting a pre-requiste tech level. There were more added Tech levels to support the 50 years added. Large nations can now become Empires which made warfare slightly easier. Annexing a Vassal has become much harder. A new option was added regarding Lucky Nations, 8 historical nations were chosen which gave them more "Luck" the player now has the option of whether or not that is added and includes a random option as well. 5 new National Idea's were added and 22 new types of Advisor was added, which made a massive impact on planning strategy.
And lastly any music file added to the Games MP3 folder is now included it in the games music which was one of the bigger requests by fans.