Where in the USA is Pretoria?

A factor that applies in reality, but the devs may or may not have accounted for, is that high-power reactors of almost any sort require considerable volumes of cooling water to turn that power into usable energy. Such a plant would almost certainly be located on the ocean, a major river, or the Great Lakes. Given the additional hassles involved with dealing with salt water, fresh is preferred; and something less vulnerable to seasonal variations would tend to favor the Great Lakes.

Given the existing shape of the US high-power distribution network, Chicago would actually be a pretty reasonable choice, although Detroit might be slightly better.

Also not conclusive by any means, but the design of Praetoria is heavy on the water features; it seems unlikely that this sort of design would have been created someplace without a major year-round water source.

But you also have to consider in-multiverse status of Earth. Paragon City contains the Terra Volta reactor, which at least powers Paragon City even despite the constant attack from supervillains. PC is explicitly in Rhode Island, and sort-of-ish a replacement for Providence. Considering game precedent and Neuron's intelligence, I don't think you can make that assumption about the location of Neuropolis.