All factions have been decided, here is the list.
faction (religion) - (title) ruler / prince - capital
Americas-4
Iroquois (pagan) - (Chief) -
Aztec (pagan) - (Emperor) Moctezuma, 16 - Tenochtitlan
Maya (pagan) - (Emperor) -
Inca (pagan) - (Emperor) Huayna Capac, 54 / Tupac Cusi Hualpa, 27 - Cusco
Africa-4
Songhai (Islam) - (Mansa) Askia Mohammad, 78 O_O... Askia Musa, 25 - Gao
Kongo (Catholic) - (Manikongo) Afonso Mvemba a Nzinga, 56 / Pedro I Nkanga a Mvemba - Mbanza-Kongo
Mutapa (Pagan) - (Mwenemutapa) Chikuyo Chisamarengu - Zvongombe
Morocco (Islam) - (Sultan) Abu Abd Allah al-Burtuqali Muhammad ibn Muhammad - Fes
Europe-13
Portugal (Catholic) - (King) Henrique, 40 - Lisboa
Spain (Catholic) - (King) Carlos I, 18 - Madrid
France (Catholic) - (King) François, 24 - Paris
HRE (Catholic but can convert through an even) - (Emperor) Maximilian, 54 - Wien
England (Protestant) - (King) Henry, 27 - London
Papal States (Catholic) - (Pope) Leo, 26 - Roma
Denmark (Protestant) - (King) Christian, 37 - Copenhagen
Hungary (Catholic) - (King) Ludvík, 12 - Prešporok
Poland-Lithuania Commonwealth (Catholic) - (King) Sigismund, 70 / Sigismund Augustus, 46 - Kraków or Warsaw
Ottoman (Islam) - (Sultan) Suleiman, 24 - Istanbul
Russia (Orthodox) - (Tsar) Vasily, 39 - Moscow
Sweden (Protestant) - (King) Gustav, 24 - Stockholm
Netherlands (Protestant and emerging faction) - (Prince) Willem, 48 / Maurits, 14 - Amsterdam
Asia-9
Mughal (Islam) - (Emperor) Zahir-ud-din Muhammad, 35 - Agra
Vijayanagara (Hinduism) - (Emperor) Krishnadevaraya, 47 - Vijayanagara
Bukahra (Islam) - (Khan) - Bukhara
Persia (Islam) - (Shāh) Ismail, 31 / Tahmasp, 4 - Tabriz.
Ming (Confucianism) - (Emperor) Zhengde, 29 / Jiajing, 9 - Nanjing
Japan (Shintoism) - (Shogun) Ashikaga Yoshitane, 52 / Ashikaga Yoshiharu, 7 - Kyoto
Korea (Confucianism) - (Jong) Yi Yeok / Yi Ho - Hanseong
Toungoo (Buddhist) - (King) Mingyinyo, 33 / Tabinshwehti, 2 - Toungoo
Açeh (Islam) - (Sultan) Ali Mughayat Syah / Salahuddin - Banda Aceh