Regions did not become damaged by looting for this long a time when I started playing in 2005. Therefore, even in the midst of war, it was still worth it to TO regions, rather than just loot them rogue. You did not need to maintain them much, other than if you had a higher taxrate than the peasants liked.
Now we loot them rogue and they have so little population left that there is no use taking them over. See Mines of Isadril for example. A very rich region on EC, but it has such a low population, and such hatred towards everyone that it would probably take half a year and plenty of work before you'd see any substantial gold coming from there. The population does not seem to be growing any either. Maybe the pop growth is put on stop when it is rogue?
And yes, Fontan is an excellent example. Although the population code has changed now (in the last 2 weeks). All Fontan regions used to increase by a mere 30-50 people per day, and now the most damaged ones increase by almost 10 times that (200-400 per day).
So that should change things a bit.
Another thing I was thinking of that is very different is starvation. Do you remember Avamar? We had at most 3 regions (Avamar city, Montijo and Oporto I believe). Long periods, we only had the city. Yet we never had problems with starvation. We didn't even talk about food in the council. It was a non-issue for some reason. Does anyone know exactly why?