I like the direction of this discussion!

Please consider these points:
Aks K said:
idea in it self is good, but I see the consequence that every square/title could contain a temple. This might be funny...
Actually, this would generally not occur, since villages themselves will never automatically try to build cultural improvements or City Halls. The player would have to order a village to do so, and upon becoming a city, would
then have the ability to begin developing itself to the next level with city improvements. Also note that villages in a city share the benefits of the city's improvements (since villages as part of a city are treated as part of the city, not as independent villages). Therefore, this consequence is possible...but only if the player wills it!
Aks K said:
I would like to have query function working on villages as well as a mapdisplay in colours of the different properties of the villages - just to get a overview.
Actually that is in my opinion what civ3 needed. More usefull statistics so one would immediately find what he/she wanted to change.
I absolutely agree--the interface should be altered to allow for viewing "layers" of information on the map to allow for easier assessment of situations and problems. In addition, the "Demographics" feature should offer more useful information.
Aks K said:
I also think of cities as an overlay on villages.
An "overlay" is a good way to describe cities. In the beginning, villages are unorganized and independent, but can later be absorbed into cities. Politically and administratively, the villages would be parts of cities, and would be affected by city-wide policies/actions. Later on, cities can then be organized in a similar fashion into provinces (by ordering the construction of a Governor's Mansion in a city to be the provincial capital). The final stage, constructing a Palace, would even more tightly bind the provinces together into one nation--one civ! In all of this, however, note that the village does not disappear--it remains the basic unit of population, and all of the other administrative entities are simply "overlays" on the villages.
Aks K said:
Thats why a settler should carry a citizen and a villager. When building the city the villager gets "consumed" by the title (just become a village under the city). The village would be able to expand to adject squares as normal.
In case this was not really clear, I mean for settlers to be composed of one population point (or one village, so building a settler is "uprooting" a village). When building a village (that may eventually become a city), the settler is "consumed" and becomes the village. When growth occurs for the village, the new population primarily consider two factors to determine settling location: productivity of land, and distance it takes to get there. Usually, then, new villages will spring up near their parent villages, but may not always be adjacent if some very attractive terrain is just a few squares away.
Aks K said:
When all titles next to a village is occupied by other villages (and the square is fully upgrated - dont know if this should be) then the village would "expand" if inside borders as a worker in the nearest city.
If outside borders then either no expansion should occur or an upgrating of the title should begin. I am in favour of the first (no expansion) - because the village is "free".
Village expansion does not limit itself to cultural or political borders (usually), so in some cases a village may expand outside of a city's cultural border, and the new village would not automatically be part of the city (the village would have to be culturally absorbed just like the original villages of the city).
Aks K said:
Also villages outside any territory can be claimed by barbarians as a dublicate warrior (meaning 1 horseman + 1 village -> 2 horsemen + 0 village).
Inside territory villages are "just" killed/looted/pillaged. This would cause an atrocity if comitted by other civs.
Barbarians are an interesting topic. I would like to see them more as "minor civs" that are not as organized as the "primary civs." Therefore, they should have culture, and that culture should determine the results of confrontation. I mention in other sections that military units "carry" the culture of the population unit they were produced from. A barbarian unit, then, carries the culture of the barbarian village/camp/city with it, and when it attacks a village outside any of the player's cultural boundaries, then the village automatically joins the barbarians (because villages have no culture by themselves--remember that culture is the mark of cities!) because the barbarian culture is greater than that of the village. If a barbarian unit attacks a village within the player's cultural bounds, then the same thing would happen if the barbarian's culture was greater. If the village's culture is greater, however, it would desperately resist the invader, although the invader would usually end up destroying the village and perhaps lose a small amount of health. These also apply to other civs, and such actions would be indeed be considered atrocities. Culture would clearly have much more effect and be much more interesting with this model!