it was never touched up in the book about different factions but it makes me think that if indianapolis was a control experiment that the variable would chance in the different cities and the only variable i could think of was faction.
It is clearly stated in Allegiant that the West Coast is "wild country" and the terrain was too rough for the government to control after the Purity War. The East is under strict government control with rationing, and heavy handed law and order. I am assuming that they mean the entire East Coast, as well as portions of the Deep South.
The Midwest is under the control of the Bureau of Genetics Welfare. The named experiment cities were: Chicago, Detroit, Indianapolis, Saint Louis, and Minneapolis. Indianapolis was a control city, which led to the breakdown in social order.
It was also stated that the other cities did not have the faction component, but after the success in Chicago, they were introduced into the other cities. The book never states in what capacity they operate at, and whether they are the same. Given that it is an experiment, it is likely that some would be the same, and others would be different.
During the book, it is unclear what experiments are left. Obviously Chicago remains, but by the end of the book, all the experiment cities have been decommissioned.