Your comments make tactical sense at the beginning of a multiple location project, especially one as complex as Sprint is trying to undertake -- start small then see if it scales up properly (make adjustments if needed). They also make sense from a critical path perspective as you noted.
But why choose one "market" for LTE upgrades versus another? Why put markets with larger populations further down the list when Sprint's stated goal is LTE available to 200 million people? AT&T and Verizon, with their larger access to capital, have often gone for major metropolitan areas first then smaller cities then towns.
Several months ago when the project plans were made, Sprint needed cash and places like the middle of Wisconsin with US Cellular may have stretched it, while also blocking satellite and other companies possible deals with these firms (http://www.telecompetitor.com/lte-will-underlie-dishntelos-fixed-wireless-broadband-service/). Even today these LTE roaming deals also have strategic advantages for Softbank by improving future chances for buyouts to further increase Sprint's market, while not increasing financial risk in case Sprint runs into trouble with NV. Of course additional factors in market selection for LTE upgrades could be contractor and equipment availability, Sprint Wimax availability/complexity, number of LTE subscribers, and the permitting delays that you mention just to name a few other possible explanations.