Essentially, flaws that are unique to and induced by scale and consolidation.
Outside of the current pandemic, those problems range from the rent-seeking consolidation of housing ownership into very few hands, to the elimination of forms of self-reliance that create healthy community — instead shifting those responsibilities to government and large institutions.
Scale also requires more top-down centralized control and regulation in order to function at all.
The issues you stated could be suburban or even rural issues, not just urban issues. In other words I think you might be conflating the difference between an agrarian economy with a modern economy with specialization, not urban vs rural.
Outside of the current pandemic, those problems range from the rent-seeking consolidation of housing ownership into very few hands, to the elimination of forms of self-reliance that create healthy community — instead shifting those responsibilities to government and large institutions.
Scale also requires more top-down centralized control and regulation in order to function at all.