I might not know what I'm talking about but as far as I know the counter-reformation began in 1545 with the Council of Trent in Italy, called by Pope Paul III, granted it wasn't that much of a reform as they only put the Inquisition back in business and adjusted the major complaints the Protestants had about the Catholic Church and that did not stop these new branches of Christianity. Game wise I see why they are different religions, even if I would prefer it to be more like the reformed paganism in CK2, what I don't get is why doesn't the Papacy gets immediately reformed (or ever in any of the bookmarks, as far as I remember) since they were the ones that began it on the first place?