@MarSus78 There are two ways (as far as I know).

Yes, one way is to wait until peace and then use the War Desire points to demand certain surrender coinditions from Your opponents. Like a shopping list and You have X amount of War Desire points  and each demand cost Y amount War Desire points. The more War desire You have, over Your opponen, the more You can demand. However there is a cap, so that you can't demand all their cities after just one war. For the AI to seek an end to the war You need to diminish their War desire, so that they sue for peace or accept You offering peace. One way to do that is to win alot of battle until You demolish their spirit to wage war against You. There are other ways too, like forgive transgretions they made against You and such. It's a bit complicated to explain without showing within the game, by maybe making a video guide. However it is possible.

The other more cheeky way is to simply ransack the city You occupy and then claim the territory again by building an oupost in it. Then You will of course lose all that was built in that region by Your opponent if wait too long as it all turns into ruins. However sometimes it's worth it. Another thing to consider is if that city came with other trerritories attached to it ??? If it did, well then those territories can revert back to their original owner(s) and You will need to recapture those as well. Also the larger the army ios that do the ransack the faster it goes. One unit can take like 27 turns, while a 4 unit army can do it in maybe 1-3 turns. Which is logical. An entire army running amokk burning down a city is faster than a single unit doing it. Another cool small detail, I think at least.

Atm there seem to be a graphical bug/glitch as well. If You ransack Your own city and then build a new city in it's tile, the art for city center and all that was removed will not become visible after You rebuild it. The city will be there, it just will not have all the pretty art again on the city center. As far as I know it's a known bug (but not 100% sure, only the devs would know for sure if it's on their fix list).

Acctually the third way, I guess, is to find all the AI's units, outposts and cities and totally wipe the AI out. However that is harder than it sounds. It can have one little scout left somewhere and still stay alive until the end (again as far as I understand it). Not sure I have ever been able to totally wipe an AI out, as I suspect they hide some unit somwhere that I have not found.

MarSus78 wrote:

OK, now I get it. So it's not like in other 4x games, that occupation end after some time, and city is back to normal. This really badly thought over. I also don't understand diplomacy, cause when I forced one to become my vassal all the cities I have captured he got back. So this is also strange.

So shit happends I will have to find every single unit they have HA HA HA (evil lough).

Well, it's more like you are an occupying force and the citizens in those cities just don't like You as long as You are at war with them. Only after a proper peace do they accept to join Your empire, or if their cultural leader is totally wiped out. Then they have no choice but to adopt Your culture and follow Your lead, as theirs is non existant anymore. :P

They probably hope for their leaders return as long as he has some units alive somewehere. :)