I'm going to give my highly local perspective on the topic, which will also be coloured by me being a historian, not an archaeologist, but I think it still might be of interest. For reasons that will become a bit clearer in a moment, I'll also put the cart before the horse and talk about what makes preservation of settlements so hard here. One of the greatest factors in the area I'm currently working in, which is southwestern (Roman) Germany and northeastern France is certainly abandonment and an end to intensive agricultural use of the area. Almost every settlement from Roman times has remained settled over the course of the last 1700 years (as the oldest cities of the area like Straßburg, Trier, Mainz or Cologne).

This leads to two main problems. The first one is re-use or spoliation of building materials, which is both a blessing and a curse. Quarrying stone is expensive, transport even more so (especially far from navigable rivers), so people looking to build or rebuild structures will naturally use that material which is available in the immediate vicinity. This is already happening in antiquity, without any large cultural breaks that might devaluate the significance or cultural connotation of a certain monument - for example, you might expect people to respect pagan cultural monuments like statues, altars and temples and not tear them down for use in building before the shift to christianity, but that is not the case. Some monuments get torn down after a generation already, and re-used for whatever seems a more pressing concern at the time.

The third and fourth centuries see lots of cities in the area that had so far been without a wall building one, and the fundaments of these walls will often be made from repurposed altars, funerary monuments, reliefs, architectural elements of temples and so on, who thus get removed from their context completely and lose a lot of information necessary for their interpretation. Of course they also get partially destroyed to make them fit the specifications of the wall. On the other hand, this leads to them being preserved for a long time, since city walls tend to be one of the longest-standing structures of a settlement, often just being expanded upon in medival and early modern times.

And when they finally get torn down for urban expansion or to accomodate revolutions in the building of fortresses, this happens during a time when humanist interest in the remains of antiquity has already awakened, and, for example at Mainz, local antiquarians are able preserve a lot of material unearthed from those walls in the late 16th and 17th century. Churches are another example where material tends to be re-used and stays in place for a long time. There are churches here in southern Germany literally built from pagan monuments, often plastered over, but now in some cases made visible. The tower of the church of Landau-Nußdorf in the Palatinate, for example, has an element from a Jupiter-column built into one of the corners, now opened to the viewer.

Other architectural elements and monuments get re-used more often or are completely destroyed by re-use, which is the case for many things made from limestone, which is burnt for lime, metals are molten down and completely unrecognizable.

The other obvious problem with continued habitation is that it is often impossible to make excavations, apart from new building projects where archeological interest has to assert itself against financial considerations from the builder, and often disinterest or even hostility from the workers who know what happens when they unearth archeological remains and report them - their schedule is ruined and pesky archeologists will take over their site. An example from Ladenburg might be illustrative here: on a building site, workers found the (complete, but fractured) remains of a Jupiter-column that had been deposited in a well, and knowing perfectly well what they had found, they started to hammer it to pieces - luckily, a neighbour saw this happening and alerted police, mayor and the local museum. The same kind of neglect and hostility almost led to the destruction or theft of the remains of the bronze elements (lions heads, busts of gods, decorative ornaments) used in the representative portal door of the forum, a really singular find for the northwestern provinces.

In this way, continued habitation makes preservation difficult for three main reasons: Re-use and destruction of ancient structures, the difficulty of excavating inhabited spaces, and sometimes disinterest or outright destruction of cultural heritage because of a conflict of interests.

So the best way to have a settlement preserved for posterity is an end of human use of the area, or at least a decrease in intensity of use. An example of the latter would be the settlements of the Vosges heights, which were small, relatively poor communities that settled on the plateaus of the northern Vosges mountains around Saverne/Zabern. It seems that they were abandoned around the 4th/5th centuries, and while some of the material was used for the newer settlements that sprung up in the river valleys below, much remained, and the area is today overgrown with forest. The structures were mainly wood, so all that's left are the fundaments and the walls of the enclosures, but since the 1960s, these have been excavated in detail, which has allowed us to get a pretty good picture of the layout of these settlements, how they were connected to each other, and how the spaces (for example cultic enclosures and small temples, funerary zones, homes) were related to each other. We can see where the monuments and cultic reliefs were situated in the space of the settlement, which is something that we are seldom able to do in most other settlements because of their re-use and spoliation.

Another way this can happen would be natural desasters, like earthquakes or volcanoes, as in the famous cases of Pompeii and Herculaneum. Volcanoes haven't been active in quite a while here along the Rhine, but Earthquakes have happened. Apart from the unfortunate circumstances they create for the inhabitants, they can be a godsend to the archeologist and historian.

Take this photo, which is really quite amazing stuff. It's the outbuilding of a Roman villa rustica, a type of medium to large farm, which fell apart during an earthquake and thus preserved the structure of the wall and its architectural makeup. The roof came down, and then the building simply fell to the sides, just in the way it had been put together, but then, even more fortuitous, the whole mess, which otherwise would surely have been used for building material, was covered by a landslide. All in all, not a good day for the farmers (though the buidling might already have been abandoned). But great for the archaeologists.

The best thing that can happen to a settlement to preserve it is ignorance or inaccessability.

Edit: typos