I don't know about permanently... the Romans planned most of their federated tribes to be relatively "permanent" affairs, and they lasted until the Roman Armies were distracted or destroyed by civil war.  And then the betrayals started.

Yep, I liked the concept of "barbarians" in the Civ games. Perhaps not all of the monsters should attack the cities, only some specific creatures. Ex.: humanoids.

Great idea! but what happens if your city is undefended, or your defenders are killed in the attack? should these monsters be able to occupy the town for a while, or stay put until driven out?  i think there should be some damaging affect the to the city its self during the raid. perhaps generated randomly, a city tile is destroyed. maybe a loss to money, materials, or people?

Well, I'm okay with scaling neutral threats, but I'd do it differently.  Eventually, I can simply seeing smaller threats being defeated but as nations expand, borders would begin to run into the territory of larger, more ancient monsters that lived deeper in the wilderness. 

Well, I would expect that your citizens would "scatter into the country side for awhile" and the monsters/ nomadic raiders would leave once they had stolen whatever they thought was valuable.  At which point, your citizens would return.  This might manifest itself ingame simply as the raiders entering the town, stealing gold, food, and killing X number of citizens, and then leaving (productivity of the city would be reduced to 0 for a certain number of turns to simulate the absence of your citizens.) 

maybe a cities prestige could be affected as well. i may be rather slow to go home if my city kept getting sacked by monsters..

I would like this idea, but it would need to be possible for monsters/individuals to attack and sack a city, not just conquer it. Why would Ogres want to run a city, after-all?

The original Civ:Colonization dealt with early indian attacks quite well, instead of 'game over' when they beat your unit the natives stole resources, burnt buildings and generally made a nuisance of themselves. In the early phase that could hamper one's efforts without meaning you have to go the military route fully so early on. Fall from Heaven 2 dealt with barbarians quite well, though I felt a more unified threat was needed. In my games Orthus the Barbarian King spawned, walked around, then died. Perhaps a game moment where all of a certain type of neutral creature banded together under a strong leader and pose a threat to all factions. An undead army that grew with each victory would be interesting,for example.

In short make neutrals as dangerous as any enemy factions rather than just a nuisance.

It can be something like in MoM ("the monsters rampage through the city and then disappear into the wilderness").