I can easily see making a slum region and dumping all the pollution heavy stuff into that one region. I like the region stuff a lot but it might ruin the single player experience if you can just make a slum region and not be forced to deal with those problems that pollution and other negative effects.
Problems can cross regional boundaries. For example, build a dirty city and the pollution will eventually cross into neighbouring cities. Have no police in a city and the criminals will start invading their neighbours.