I think initially when the supercharger rollout began they purposely avoided the cities with the intent of "superchargers for long distance travel". I believe they have changed their philosophy somewhat and will hit the big cities after they get most of the gaps filled in on the interstates. I believe they realize that by the time Model 3 comes out and with their target sales of 500,000/yr that the demographic of buyers will shift with many of those sales going to city dwellers who don't have a reasonable place to charge at home.
I think they should keep avoiding cities for a while longer!
The opening text of the Supercharger page on tesla.com implies that placement will be on routes that enable long distance travels:
"Stations are strategically placed to minimize stops during long distance travel and are conveniently located near restaurants, shopping centers, and WiFi hot spots."
Despite that, a considerable number of them have been placed at destinations, including both cities and other types of travel end-points. A recent example is the one under construction in Southampton NY, out toward the end of Long Island.
Clearly there are a great many factors that influence the rate at which any given supercharger reaches completion, once targeted. And there are probably a number of political aspects that go into the targeting of specific sites. Still, given the concerns that Tesla has expressed about excessive dependence on superchargers by local residents, one may question the priority that is being given to locations on major interstate highways. All parts of the country have their local concerns with this, and mine are with I-76, I-80, and I-86 across western NY and PA.
It seems to me that these major connectors of destinations should be prioritized and populated (≤ 200 miles apart) before cities and other destinations and before capacity becomes a priority along heavily travelled routes.