I have done some search abouth the issues. Here are the problem I identify:
1. Some civilization don't get proper city names.
With the help of this program - "Duplicates Finder" I found few entries that appear both in ...\MODS\Anno Domini (Gods and Kings) (v 4)\XML\GameInfo\CityNames.xml and in ...Assets\DLC\Expansion2\Gameplay\XML\Text\en_US\CIV5GameTextInfos_Cities_Expansion2.xml I deleted the entries from the first file and now all civilizations have proper names
Problem resolved!!
2. Some city states don't get proper leaders - when you open the communication window, you get error message that some .dds file is missing.
Open file ...\MODS\Anno Domini (Gods and Kings) (v 4)\XML\GameInfo\MinorCivLeaders.sql and delete all line with .dds files, that are not in the folder ...\MODS\Anno Domini (Gods and Kings) (v 4)\Art\CityStateLeaders\
Problem resolved!!
3. Many wonders don't get proper text (names, descriptions, pedia entries..)
It seems there is some duplication of entries for the Parthenon wonder. Just rename all text keys for that wonder like that ..._PARTHENON... to ..._PARTHENONMOD... (for example) in the following files: Buildings.xml, WondersText.xml, BuildingClass.xml.
Problem resolved!!
4. Many city states don't get proper city names
I searched for duplicates, but could not find any. If someone could help here, it will be greatly appreciated!!
Problem not resolved, yet
On sidenote: How to remove Christianity and Islaam?