I'm impressed at how much thought you're putting into this. I myself tend to put a bit of thought into the names, but not as much as I might put into some other aspects. I go with the trends (more or less in order of frequency) of most places being named after a local geographic feature, many are named after people, some are named after industry, a few are named after royalty, etc.

And different regions could get different language/dialects to add more flavour, of course.
Prairie View (town on a hill near a large plain)
Crystal Falls (village near a waterfall)
Redriver (city along a river gorge cutting through an iron deposit making the water go reddish)
Johan's Gap (town in a mountain pass)
Port Edward (seaport)
Prince George (some random town somewhere)
Sawyerville (town in the woods with a dependance on logging)

Etc.

Then for fun, run the names in one of your regions through an online translator to give a local feel:

Opinião da pradaria
Quedas de cristal
Rio vermelho
Johan's passa
Edward portuário
Príncipe George
Cidade da serração

It's actually kind of fun once you get going