I have gone through very interesting hundred years. At least from 1700 to 1800 I had a kind of an Golden Age (but not in Gameplay terms).
Since I acquired Rome, Pompeii, Caralis (Sardinia/Corsica), Appolonia (Balkans) and finally Mediolanum (thanks to a Congress) my stability is rising like hell. I had been in collapsing stage in 1700 (and certainly was only saved by Hereditary Rule - I already had pop-ups like:"Your empire is declining into Civil War" but nothing happened) but now in 1800 I am stable ! I mean stable like not unstable , shaky etc. That means 3 stages higher than collapsing !
When I reached the shaky stage I risked a revolution to Universal Suffrage (which I wanted to avoid before because of the transitory period) and Emancipation.
I had to decide which civisc to change (because I wanted only 2 civics to change but there were 4 outdated ones, Hereditary Rule, Slavery, Bureaucracy and Organized Religion) and finally I settled for replacing Hereditary Rule and Slavery. I went for Universal Suffrage, because Representation is not fitting for my large empire (in the same way like Bureaucracy is not fitting)
In anyway this boosted my stability even further.
I am currently running : Universal Suffrage, Bureaucracy, Emancipation, Free Market, Organized Religion and Viceroyalty with 2 vassals. (so basically now I am the Modern Russian Federation

- not bad for the moment)
Now I am planning for my Golden Age (with Olympic Park) to make then the final shift to Free Speech and Free Religion. [Can you imaging the American way of life in the crowded streets of Egypt? What am I doing ? Will Al-Quaeda now knock at my door ??]
In any way thanks for the links that was definitively veeery helpful !
Especially since I came to know that Organized Religion is certainly the reason for my bad ratings in cities - In Egypt, North Africa and Yerusalem I was running up to 3 religions (Christianity - my hammer providing state religion, Judaism - my money religion and Islam) in order to protect my territory from Turkish, Arabian, Spanish and Roman Culture.
Now I came to know that Organized Religion is giving instability when there are several religions in your cities ..
In anyway I am now waiting for the rebirth of Egypt. As I am quite happy with my Western Mediterrean Territory I am planning to vassalize Egypt and to give them at least half of Egypt.
I am not sure though where to draw the line and whether to keep Yerusalem.
On the one hand, Yerusalem is under heavy cultural pressure from Turkey, which controls the whole area north and north east of Yerusalem, and Arabia, which controls the whole area south and south east of Yerusalem.
Therefore Yerusalem will always be an island city, but on the other hand I have invested heavily in this eastern border of my civilization. One Great Prophet, one Great Artist (who got kind of ridiculed because soon later the Turks conquered Athene which somehow even converted the just built-up culture in Yerusalem as well), lots of money on Mosques, Synagoges, Cathedrals and numerous Jewish Missionaries.
So I have two scenarios. Currently there are 4 cities that would flip:
Cyrenaica, Port Said (that located east of the Nile on the Mediterrean Shore), Niwt-Rst and East Chad (that is located between the Chad Lake and the Nile)
The cities that won't be affected would be the whole area west of Cyrenaica + Eritrea (that is located on the Red Sea just northeast of the northern Nile Lake and northwest of the cows) and Yerusalem.
Now I could conquer Cyrenaica, Port Said and Niwt-Rst in order to vassalize Egypt but then gift back Niwt-Rst and Eritrea. In this case I would keep the whole Mediterrean Shore but get rid of 3 cities from my slightly over-expanded empire.
Or I just conquer Cyrenaica and stay west of the Nile and gift the Egypts Yerusalem and Eritrea, so then I would get rid of 5 cities but also lose my precious gem Yerusalem ..
What would you do ? I do not want to keep an isolated Yerusalem, because even despite that I am having open borders with the Turks now doesnt mean I will have them for long ..